Fri Feb 7 09:39:23 UTC 2025 I: starting to build aegean/trixie/amd64 on jenkins on '2025-02-07 09:39' Fri Feb 7 09:39:23 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_14/31579/console.log Fri Feb 7 09:39:23 UTC 2025 I: Downloading source for trixie/aegean=0.16.0+dfsg-4 --2025-02-07 09:39:23-- http://deb.debian.org/debian/pool/main/a/aegean/aegean_0.16.0%2bdfsg-4.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2235 (2.2K) [text/prs.lines.tag] Saving to: ‘aegean_0.16.0+dfsg-4.dsc’ 0K .. 100% 394M=0s 2025-02-07 09:39:23 (394 MB/s) - ‘aegean_0.16.0+dfsg-4.dsc’ saved [2235/2235] Fri Feb 7 09:39:23 UTC 2025 I: aegean_0.16.0+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: aegean Binary: aegean Architecture: amd64 arm64 armel armhf i386 mipsel powerpc ppc64el s390x hurd-i386 kfreebsd-amd64 kfreebsd-i386 ppc64 x32 Version: 0.16.0+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://standage.github.io/AEGeAn Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/aegean Vcs-Git: https://salsa.debian.org/med-team/aegean.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: debhelper-compat (= 13), libcairo2-dev, libgenometools0-dev, python3 Package-List: aegean deb science optional arch=amd64,arm64,armel,armhf,i386,mipsel,powerpc,ppc64el,s390x,hurd-i386,kfreebsd-amd64,kfreebsd-i386,ppc64,x32 Checksums-Sha1: 29ba01d6ae8ec73e90a3dcea4cc1496dbe332ad1 534860 aegean_0.16.0+dfsg.orig.tar.xz 00691a8e3c55341d06cb35f66476e5f4b0a23426 9628 aegean_0.16.0+dfsg-4.debian.tar.xz Checksums-Sha256: 8d60ba13c60d404d04746c2f1253a712392f8368806d93f01f8e6edb0ec9c039 534860 aegean_0.16.0+dfsg.orig.tar.xz 18eaae267e4af9c076ea1679286b71f8a242d7e2124d09eb2457acd07b8e1f93 9628 aegean_0.16.0+dfsg-4.debian.tar.xz Files: 8df4e46ed3a5e4a5e1a5d863e03ba3c9 534860 aegean_0.16.0+dfsg.orig.tar.xz e15b076adebc76512ba2fa37111644de 9628 aegean_0.16.0+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmYK+dUACgkQ6NN64vCf SHL84Q/9EJ2IxMBQLppk130OADeeDNlfTrNi5u1BNGwvbm+qnrIABCd5wV5VdLss jegnAftFHvy+dmakYTZqM1DogE3c+XLrGn26Fnl6TZ2DL4OVI0UiLZXoT/6xOR8e z0elbB9qyithsrtOsMVh+cYdTedhRljSEZXYhN8TWV9gMcII2DXshWKIkmYm3Oyx F1i8c4HLb2Sa1XFwxfKqaf4CnGrVZgFLi3mBV/OAhFXPDqLtTZUadG94RYqDEsWL I3WsXRmFVtiK/1BOXZoAxsAbe5uFPKD6oU+8yQKcc/iRCN1OHihhrfsHurJbJdDX tmOhgCtysThLDr9qxvZUCakZT+nsfvTPNHMVdjTkUshD+KCc1mOxZ2wblRtCGtPB VrmSnoVIU/hRTp34mOD2ZLMLAVRb3cdG0rjV7sVf5bmgDPC6lSCqfyhjoldzayzK QV6xvoZAQTW36MPERsTEsPZ0RAhhgw9950fiYIc+8oENg0t6gf+iQLqlMFN7B4iz ryvmYHOfUGTDaO7sfbvgzG0TjGiDewjVPwvrKMFLsy/yaD7kirLb8h1aqUX7Tn4Z vsNM6msxlO9sfFmoepdNU0smaga7RToZ2PLpL8ZEGtjak7iCSJIjxJsdJxdTnt7X HbXYIkrXflW/vuH6ungp2BVcKV5pz+AjL827y2YxOykpcmDqXnw= =zDYg -----END PGP SIGNATURE----- Fri Feb 7 09:39:23 UTC 2025 I: Checking whether the package is not for us Fri Feb 7 09:39:23 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Fri Feb 7 09:39:23 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Fri Feb 7 09:40:08 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Mar 12 04:02:24 -12 2026 I: pbuilder-time-stamp: 1773331344 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 [aegean_0.16.0+dfsg-4.dsc] I: copying [./aegean_0.16.0+dfsg.orig.tar.xz] I: copying [./aegean_0.16.0+dfsg-4.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./aegean_0.16.0+dfsg-4.dsc: unsupported subcommand dpkg-source: info: extracting aegean in aegean-0.16.0+dfsg dpkg-source: info: unpacking aegean_0.16.0+dfsg.orig.tar.xz dpkg-source: info: unpacking aegean_0.16.0+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_hardening dpkg-source: info: applying fix_m64_on_some_archs dpkg-source: info: applying remove_license dpkg-source: info: applying adjust_datapath dpkg-source: info: applying follow_links dpkg-source: info: applying includepaths dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/724579/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='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='ee8a0d99e8a844a9834d002dffddd040' 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='724579' 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.Wl9viYud/pbuilderrc_wUch --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.Wl9viYud/b1 --logfile b1/build.log aegean_0.16.0+dfsg-4.dsc' SUDO_GID='110' SUDO_UID='105' 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 ionos5-amd64 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/724579/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), libcairo2-dev, libgenometools0-dev, python3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19842 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libcairo2-dev; however: Package libcairo2-dev is not installed. pbuilder-satisfydepends-dummy depends on libgenometools0-dev; however: Package libgenometools0-dev is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 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} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} genometools-common{a} gettext{a} gettext-base{a} girepository-tools{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblkid-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo-gobject2{a} libcairo-script-interpreter2{a} libcairo2{a} libcairo2-dev{a} libdatrie1{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig-dev{a} libfontconfig1{a} libfreetype-dev{a} libfreetype6{a} libfribidi0{a} libgenometools0-dev{a} libgenometools0t64{a} libgio-2.0-dev{a} libgio-2.0-dev-bin{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgraphite2-3{a} libharfbuzz0b{a} libice-dev{a} libice6{a} libicu72{a} liblua5.1-0{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libmount-dev{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpixman-1-dev{a} libpkgconf3{a} libpng-dev{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libselinux1-dev{a} libsepol-dev{a} libsm-dev{a} libsm6{a} libsysprof-capture-4-dev{a} libthai-data{a} libthai0{a} libtool{a} libtre5{a} libuchardet0{a} libunistring5{a} libx11-6{a} libx11-data{a} libx11-dev{a} libxau-dev{a} libxau6{a} libxcb-render0{a} libxcb-render0-dev{a} libxcb-shm0{a} libxcb-shm0-dev{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxml2{a} libxrender-dev{a} libxrender1{a} lua-md5{a} m4{a} man-db{a} media-types{a} native-architecture{a} netbase{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3-packaging{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} uuid-dev{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl libpng-tools lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 132 newly installed, 0 to remove and 0 not upgraded. Need to get 49.4 MB of archives. After unpacking 181 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.13-minimal amd64 3.13.1-3+b1 [859 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.13-minimal amd64 3.13.1-3+b1 [2203 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-6 [257 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libpython3.13-stdlib amd64 3.13.1-3+b1 [1973 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 python3.13 amd64 3.13.1-3+b1 [740 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.4-2 [92.1 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.17-3 [862 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libtool all 2.5.4-3 [539 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.1-1 [8584 B] Get: 36 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.23.1-1 [1680 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.24.1 [920 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.46-4 [284 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-2 [463 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 liblua5.1-0 amd64 5.1.5-10 [110 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.4-2 [1502 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libtre5 amd64 0.9.0-1 [50.0 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 genometools-common all 1.6.5+ds-2.2 [195 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 native-architecture all 0.2.5 [2204 B] Get: 78 http://deb.debian.org/debian trixie/main amd64 libgirepository-2.0-0 amd64 2.82.4-2 [139 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 girepository-tools amd64 2.82.4-2 [145 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 uuid-dev amd64 2.40.4-2 [47.5 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libblkid-dev amd64 2.40.4-2 [204 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libcairo-script-interpreter2 amd64 1.18.2-2 [58.8 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libpng-dev amd64 1.6.46-4 [370 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libfontconfig-dev amd64 2.15.0-2 [414 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libffi-dev amd64 3.4.6-1 [60.6 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libsepol-dev amd64 3.7-1 [370 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libpcre2-16-0 amd64 10.44-5 [260 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libpcre2-32-0 amd64 10.44-5 [248 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libpcre2-posix3 amd64 10.44-5 [60.4 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libpcre2-dev amd64 10.44-5 [790 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libselinux1-dev amd64 3.7-3.1 [160 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libmount-dev amd64 2.40.4-2 [29.4 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libsysprof-capture-4-dev amd64 47.2-1 [47.7 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libgio-2.0-dev amd64 2.82.4-2 [1677 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libglib2.0-data all 2.82.4-2 [1276 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libglib2.0-bin amd64 2.82.4-2 [127 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libgio-2.0-dev-bin amd64 2.82.4-2 [163 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libglib2.0-dev-bin amd64 2.82.4-2 [52.1 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libglib2.0-dev amd64 2.82.4-2 [52.9 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libpixman-1-dev amd64 0.44.0-3 [11.4 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+24 [217 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 x11proto-core-dev all 2024.1-1 [3312 B] Get: 118 http://deb.debian.org/debian trixie/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libxcb-render0-dev amd64 1.17.0-2+b1 [118 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0-dev amd64 1.17.0-2+b1 [108 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libxext-dev amd64 2:1.3.4-1+b3 [104 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b4 [35.8 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libcairo2-dev amd64 1.18.2-2 [43.0 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 lua-md5 amd64 1.2+git+1+8d87fee-2+b2 [13.7 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 libgenometools0t64 amd64 1.6.5+ds-2.2 [1420 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 libgenometools0-dev amd64 1.6.5+ds-2.2 [95.2 kB] Fetched 49.4 MB in 4s (12.7 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (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 ... 19842 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3+b1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3+b1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.1-3+b1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.1-3+b1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.1-3+b1_amd64.deb ... Unpacking python3.13 (3.13.1-3+b1) ... 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Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up netbase (6.4) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.1-1) ... Setting up libblkid-dev:amd64 (2.40.4-2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up gettext (0.23.1-1) ... Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up libpcre2-dev:amd64 (10.44-5) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b4) ... Setting up libice-dev:amd64 (2:1.1.1-1) ... Setting up libtool (2.5.4-3) ... Setting up libselinux1-dev:amd64 (3.7-3.1) ... Setting up fontconfig-config (2.15.0-2) ... Setting up libpng-dev:amd64 (1.6.46-4) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libffi-dev:amd64 (3.4.6-1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up libxdmcp-dev:amd64 (1:1.1.5-1) ... Setting up libglib2.0-0t64:amd64 (2.82.4-2) ... No schema files found: doing nothing. Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-1) ... Setting up groff-base (1.23.0-7) ... Setting up libharfbuzz0b:amd64 (10.2.0-1) ... Setting up libfontconfig1:amd64 (2.15.0-2) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-3+b1) ... Setting up libmount-dev:amd64 (2.40.4-2) ... Setting up libpython3-stdlib:amd64 (3.13.1-2) ... Setting up fontconfig (2.15.0-2) ... Regenerating fonts cache... done. Setting up libgio-2.0-dev:amd64 (2.82.4-2) ... Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up python3.13 (3.13.1-3+b1) ... Setting up libgirepository-2.0-0:amd64 (2.82.4-2) ... Setting up libsm-dev:amd64 (2:1.2.4-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.56.1-1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up libglib2.0-bin (2.82.4-2) ... Setting up python3 (3.13.1-2) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libfreetype-dev:amd64 (2.13.3+dfsg-1) ... Setting up libxcb-shm0-dev:amd64 (1.17.0-2+b1) ... Setting up python3-packaging (24.2-1) ... Setting up libxcb-render0-dev:amd64 (1.17.0-2+b1) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b3) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libpangoft2-1.0-0:amd64 (1.56.1-1) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b4) ... Setting up libpangocairo-1.0-0:amd64 (1.56.1-1) ... Setting up libcairo-script-interpreter2:amd64 (1.18.2-2) ... Setting up libgio-2.0-dev-bin (2.82.4-2) ... Setting up girepository-tools:amd64 (2.82.4-2) ... Setting up libfontconfig-dev:amd64 (2.15.0-2) ... Setting up debhelper (13.24.1) ... Setting up genometools-common (1.6.5+ds-2.2) ... Setting up libglib2.0-dev-bin (2.82.4-2) ... Setting up libglib2.0-dev:amd64 (2.82.4-2) ... Setting up libgenometools0t64 (1.6.5+ds-2.2) ... Setting up libcairo2-dev:amd64 (1.18.2-2) ... Setting up libgenometools0-dev (1.6.5+ds-2.2) ... Processing triggers for libc-bin (2.40-6) ... 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/aegean-0.16.0+dfsg/ && 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 > ../aegean_0.16.0+dfsg-4_source.changes dpkg-buildpackage: info: source package aegean dpkg-buildpackage: info: source version 0.16.0+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_auto_clean make -j42 clean make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' rm -rf bin/parseval bin/canon-gff3 bin/locuspocus bin/gaeval bin/xtractore bin/pmrna bin/tidygff3 bin/unittests libaegean.a obj/AgnAttributeFilterStream.o obj/AgnCliquePair.o obj/AgnCompareReportHTML.o obj/AgnCompareReportText.o obj/AgnComparison.o obj/AgnFilterStream.o obj/AgnGaevalVisitor.o obj/AgnGeneStream.o obj/AgnInferCDSVisitor.o obj/AgnInferExonsVisitor.o obj/AgnInferParentStream.o obj/AgnLocus.o obj/AgnLocusFilterStream.o obj/AgnLocusMapVisitor.o obj/AgnLocusRefineStream.o obj/AgnLocusStream.o obj/AgnMrnaRepVisitor.o obj/AgnPseudogeneFixVisitor.o obj/AgnRemoveChildrenVisitor.o obj/AgnTranscriptClique.o obj/AgnTypecheck.o obj/AgnUnitTest.o obj/AgnUtils.o inc/core/AgnVersion.h bin/*.dSYM make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' rm -f /build/reproducible-path/aegean-0.16.0+dfsg/README make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_auto_build -- prefix=/build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp 64bit=yes errorcheck=no make -j42 "INSTALL=install --strip-program=true" prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp 64bit=yes errorcheck=no make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' [print inc/core/AgnVersion.h] /build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:31: SyntaxWarning: invalid escape sequence '\S' sha1match = re.search('commit (\S+)', logout) /build/reproducible-path/aegean-0.16.0+dfsg/data/scripts/version.py:37: SyntaxWarning: invalid escape sequence '\s' yearmatch = re.search('Date:\s+.+(\d{4}) ', logout) [compile AgnAttributeFilterStream] [compile AgnCliquePair] [compile AgnCompareReportHTML] [compile AgnCompareReportText] [compile AgnComparison] [compile AgnFilterStream] [compile AgnGaevalVisitor] [compile AgnGeneStream] [compile AgnInferCDSVisitor] [compile AgnInferExonsVisitor] [compile AgnInferParentStream] [compile AgnLocus] [compile AgnLocusFilterStream] [compile AgnLocusMapVisitor] [compile AgnLocusRefineStream] [compile AgnLocusStream] [compile AgnMrnaRepVisitor] [compile AgnPseudogeneFixVisitor] [compile AgnRemoveChildrenVisitor] [compile AgnTranscriptClique] src/core/AgnCompareReportText.c: In function ‘compare_report_text_comp_class_summary’: src/core/AgnCompareReportText.c:287:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 287 | strncpy(header + 4, label, strlen(label)); | ^ src/core/AgnCompareReportText.c:287:3: note: length computed here 287 | strncpy(header + 4, label, strlen(label)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [compile AgnTypecheck] [compile AgnUnitTest] [compile AgnUtils] src/core/AgnCompareReportText.c: In function ‘compare_report_text_summary_struc’: src/core/AgnCompareReportText.c:589:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 589 | strncpy(buffer + 14, units, strlen(units)); | ^ src/core/AgnCompareReportText.c:589:3: note: length computed here 589 | strncpy(buffer + 14, units, strlen(units)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ src/core/AgnCompareReportText.c:599:3: warning: ‘__builtin___strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 599 | strncpy(buffer + 15, units, strlen(units)); | ^ src/core/AgnCompareReportText.c:599:3: note: length computed here 599 | strncpy(buffer + 15, units, strlen(units)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [compile ParsEval] [compile CanonGFF3] [compile LocusPocus] [compile GAEVAL] [compile Xtractore] [compile bin/pmrna] [compile bin/tidygff3] [create libaegean] [compile unit tests] ar: `u' modifier ignored since `D' is the default (see `U') ar: creating libaegean.a make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_auto_test -- useshared=yes 64bit=yes testthreads=5 make -j42 test useshared=yes 64bit=yes testthreads=5 make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' AEGeAn Unit Tests AEGeAn::AgnAttributeFilterStream | SUCCESS | Pogonomyrmex barbatus (partial) | PASS AEGeAn::AgnPseudogeneFixVisitor | SUCCESS | Gene, no pseudo attribute | PASS | Gene, bogus pseudo attribute | PASS | Corrected pseudogene | PASS | Uncorrected pseudogene | PASS | iLocus with gene & pseudogene | PASS AEGeAn::AgnInferParentStream | SUCCESS | Test 1: basic | PASS | Test 2: 2 top-level | PASS | Test 3: 2 top-level, inferred parent | PASS | Test 4: multichild | PASS | Test 5: multichild, inferred parent | PASS AEGeAn::AgnMrnaRepVisitor | SUCCESS | TAIR10: test 1 | PASS AEGeAn::AgnRemoveChildrenVisitor | SUCCESS | Test 1: grape (Gaze) | PASS AEGeAn::AgnTranscriptClique | SUCCESS | simple check | PASS | two mRNAs | PASS | copy check | PASS AEGeAn::AgnCliquePair | SUCCESS | perfect match vs. self | PASS | CDS match | PASS | non-match | PASS AEGeAn::AgnLocus | SUCCESS | grape test 1 | PASS | grape test 2 | PASS | filter by CDS length | PASS | filter by exon number | PASS AEGeAn::AgnFilterStream | SUCCESS | mRNA | PASS | exon | PASS | CDS | PASS | intron | PASS | exon+intron | PASS | CDS+intron | PASS AEGeAn::AgnInferCDSVisitor | SUCCESS | grape test sans UTRs | PASS | grape test with UTRs, strand check | PASS | grape test 3 | PASS | grape test 4 | PASS AEGeAn::AgnInferExonsVisitor | SUCCESS | grape test sans UTRs | PASS | grape test with UTRs, strand check | PASS | grape test 3 | PASS | grape test 4 | PASS AEGeAn::AgnGeneStream | SUCCESS | 1 gene, 2 mRNAs | PASS | 1 gene, 2 mRNAs (one sans CDS) | PASS | mRNA only | PASS | mRNA boundaries | PASS AEGeAn::AgnLocusStream | SUCCESS | grape test (pairwise) | PASS | Pdom test (pairwise) | PASS | Amel test (Augustus) | PASS | Delta=200 | PASS AEGeAn::AgnLocusRefineStream | SUCCESS | Atta cephalotes (syndrome): coords | PASS | Atta cephalotes (syndrome): elen | PASS | Megachile rotundata CST: coords | PASS | Megachile rotundata CST: elen | PASS AEGeAn::AgnGaevalVisitor | SUCCESS | range intersect (1) | PASS | range intersect (2) | PASS | range intersect (3) | PASS | union (1) | PASS | union (2) | PASS | union (3) | PASS | intersect (1) | PASS | intersect (2) | PASS | intersect (3) | PASS | intersect (4) | PASS | intersect (5) | PASS | calculate coverage | PASS | introns confirmed (no gaps) | PASS | introns confirmed (gaps) | PASS | calculate integrity | PASS ===== Unit tests passed for all 15 classes! ===== AEGeAn Functional Tests GFF3 I/O: 'AT1G05320' | codons | PASS | sansexons | PASS | sansutrs | PASS | withprot | PASS GFF3 I/O: 'FBgn0035002' | codons | PASS | sansexons | PASS | sansutrs | PASS AEGeAn::LocusPocus | default | PASS | end skip | PASS | Apis mellifera plap | PASS | Apis mellifera plap (CDS) | PASS | Apis mellifera LSM | PASS | Megachile rotundata CST (intron) | PASS | iiLocus lengths (Amel OGS Group7.16) | PASS | Nasonia vitripennis (intron gene) | PASS | A. echinatior (intron gene + ncRNA) | PASS AEGeAn::Xtractore | major royal jelly | PASS AEGeAn::CanonGFF3 | A. mellifera gene multitrans | PASS AEGeAn::GAEVAL | sans CDS | PASS | Pdom | PASS AEGeAn::ParsEval | Amel Group7.16 (text) | PASS | Amel Group7.16 (delta=500) | PASS | Amel Group7.16 (HTML) | PASS AEGeAn::align-convert.py | GAEVAL example1 | PASS | GAEVAL example5 | PASS AEGeAn::pmrna | A. mellifera Shal | PASS | A. mellifera dock | PASS | A. mellifera pseudo | PASS AEGeAn::tidygff3 | A. dorsata exception | PASS make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_auto_install -- 64bit=yes prefix=/build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp make -j42 install DESTDIR=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/aegean AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" 64bit=yes prefix=/build/reproducible-path/aegean-0.16.0\+dfsg/debian/tmp make[2]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' cp bin/parseval bin/canon-gff3 bin/locuspocus bin/gaeval bin/xtractore bin/pmrna bin/tidygff3 /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/bin/. cp libaegean.a /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/lib/. cp inc/core/*.h /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/include/aegean/. cp -r data/share/* /build/reproducible-path/aegean-0.16.0+dfsg/debian/tmp/share/aegean/. make[2]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_install debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' cp /build/reproducible-path/aegean-0.16.0+dfsg/README.md /build/reproducible-path/aegean-0.16.0+dfsg/README dh_installdocs make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms debian/rules override_dh_missing make[1]: Entering directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_missing --list-missing dh_missing: warning: bin/canon-gff3 exists in debian/tmp but is not installed to anywhere (related file: "bin/canon-gff3") dh_missing: warning: bin/gaeval exists in debian/tmp but is not installed to anywhere (related file: "bin/gaeval") dh_missing: warning: bin/locuspocus exists in debian/tmp but is not installed to anywhere (related file: "bin/locuspocus") dh_missing: warning: bin/parseval exists in debian/tmp but is not installed to anywhere (related file: "bin/parseval") dh_missing: warning: bin/pmrna exists in debian/tmp but is not installed to anywhere (related file: "bin/pmrna") dh_missing: warning: bin/tidygff3 exists in debian/tmp but is not installed to anywhere (related file: "bin/tidygff3") dh_missing: warning: bin/xtractore exists in debian/tmp but is not installed to anywhere (related file: "bin/xtractore") dh_missing: warning: include/aegean/AgnAttributeFilterStream.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnCliquePair.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnCompareReportHTML.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnCompareReportText.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnComparison.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnFilterStream.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnGaevalVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnGeneStream.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnInferCDSVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnInferExonsVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnInferParentStream.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnLocus.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnLocusFilterStream.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnLocusMapVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnLocusRefineStream.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnLocusStream.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnMrnaRepVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnPseudogeneFixVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnRemoveChildrenVisitor.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnTranscriptClique.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnTypecheck.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnUnitTest.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnUtils.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/AgnVersion.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: include/aegean/aegean.h exists in debian/tmp but is not installed to anywhere dh_missing: warning: lib/libaegean.a exists in debian/tmp but is not installed to anywhere While detecting missing files, dh_missing noted some files with a similar name to those that were missing. This warning /might/ be resolved by replacing references to the missing files with the similarly named ones that dh_missing found - assuming the content is identical. As an example, you might want to replace: * bin/canon-gff3 with: * bin/canon-gff3 in a file in debian/ or as argument to one of the dh_* tools called from debian/rules. (Note it is possible the paths are not used verbatim but instead directories containing or globs matching them are used instead) Alternatively, add the missing file to debian/not-installed if it cannot and should not be used. The following debhelper tools have reported what they installed (with files per package) * dh_install: aegean (8) * dh_installdocs: aegean (1) * dh_installman: aegean (7) If the missing files are installed by another tool, please file a bug against it. When filing the report, if the tool is not part of debhelper itself, please reference the "Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+). (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz) Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built If the omission is intentional or no other helper can take care of this consider adding the paths to debian/not-installed. make[1]: Leaving directory '/build/reproducible-path/aegean-0.16.0+dfsg' dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'aegean-dbgsym' in '../aegean-dbgsym_0.16.0+dfsg-4_amd64.deb'. dpkg-deb: building package 'aegean' in '../aegean_0.16.0+dfsg-4_amd64.deb'. dpkg-genbuildinfo --build=binary -O../aegean_0.16.0+dfsg-4_amd64.buildinfo dpkg-genchanges --build=binary -O../aegean_0.16.0+dfsg-4_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/724579 and its subdirectories I: Current time: Thu Mar 12 04:03:07 -12 2026 I: pbuilder-time-stamp: 1773331387 Fri Feb 7 09:40:08 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Fri Feb 7 09:40:08 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Fri Feb 7 09:43:14 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Fri Feb 7 09:43:14 UTC 2025 I: aegean_0.16.0+dfsg-4_amd64.changes: Format: 1.8 Date: Mon, 01 Apr 2024 19:49:51 +0200 Source: aegean Binary: aegean aegean-dbgsym Architecture: amd64 Version: 0.16.0+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: aegean - integrated genome analysis toolkit Closes: 1068178 Changes: aegean (0.16.0+dfsg-4) unstable; urgency=medium . * Remove explicit runtime dependency on libgenometools0. Closes: #1068178 * Add d/copyright information for debian/ directory. * Bump Standards-Version. * Add Rules-Requires-Root: no. * Update debhelper compat level to 13. * Only list files not installed. * Adjust renamed lintian tag overrides. * Bump watchfile version to 4. Checksums-Sha1: 704f8a305c3a0555504e248e56ea6728c944dad8 1317028 aegean-dbgsym_0.16.0+dfsg-4_amd64.deb 99ff211c020e1077cefc5baad3f96f155fb40b8e 8186 aegean_0.16.0+dfsg-4_amd64.buildinfo 061d07c03c7d99367f314468b239294e178177a3 218028 aegean_0.16.0+dfsg-4_amd64.deb Checksums-Sha256: 6d61419d2d415f6eda307aa37442a32fefe904093fc57e84eb022a59657bcb45 1317028 aegean-dbgsym_0.16.0+dfsg-4_amd64.deb 27cb6be548ba07db2ac4e89dd9e4c69de707cf5da19f48a4e866e7dfce653364 8186 aegean_0.16.0+dfsg-4_amd64.buildinfo 9d083305a472b73c22aebda722d8a1d9238a69c0fb29966ed109dc9baf8b4259 218028 aegean_0.16.0+dfsg-4_amd64.deb Files: 4f9090e9e83717c6c3fee0ee7484e5db 1317028 debug optional aegean-dbgsym_0.16.0+dfsg-4_amd64.deb 8d20402f8c18664e630ab0980dc3d812 8186 science optional aegean_0.16.0+dfsg-4_amd64.buildinfo 770c391cd25e1f45ab81074894dde8b7 218028 science optional aegean_0.16.0+dfsg-4_amd64.deb Fri Feb 7 09:43:15 UTC 2025 I: diffoscope 287 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_14-31579.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Wl9viYud/aegean_0.16.0+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Wl9viYud/aegean_0.16.0+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Wl9viYud/aegean_0.16.0+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Wl9viYud/b1/aegean_0.16.0+dfsg-4_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Wl9viYud/b2/aegean_0.16.0+dfsg-4_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 Service runtime: 220ms CPU time consumed: 221ms Fri Feb 7 09:43:16 UTC 2025 I: diffoscope 287 found no differences in the changes files, and a .buildinfo file also exists. Fri Feb 7 09:43:16 UTC 2025 I: aegean from trixie built successfully and reproducibly on amd64. Fri Feb 7 09:43:17 UTC 2025 I: Submitting .buildinfo files to external archives: Fri Feb 7 09:43:17 UTC 2025 I: Submitting 12K b1/aegean_0.16.0+dfsg-4_amd64.buildinfo.asc Fri Feb 7 09:43:20 UTC 2025 I: Submitting 12K b2/aegean_0.16.0+dfsg-4_amd64.buildinfo.asc Fri Feb 7 09:43:22 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Feb 7 09:43:22 UTC 2025 I: Done submitting .buildinfo files. Fri Feb 7 09:43:22 UTC 2025 I: Removing signed aegean_0.16.0+dfsg-4_amd64.buildinfo.asc files: removed './b1/aegean_0.16.0+dfsg-4_amd64.buildinfo.asc' removed './b2/aegean_0.16.0+dfsg-4_amd64.buildinfo.asc'