Running as unit: rb-build-amd64_29-25892.service ==================================================================================== Thu Nov 21 01:55:43 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_29) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Thu Nov 21 01:55:43 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-2m4tqreU" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 01:55:43 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Nov 21 01:55:43 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-khmMTp' Thu Nov 21 01:55:43 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Nov 21 01:55:43 UTC 2024 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-Oc5gEt' ok, let's check if rnahybrid is building anywhere yet… ok, rnahybrid is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of rnahybrid in trixie on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Thu Nov 21 01:55:55 UTC 2024 I: starting to build rnahybrid/trixie/amd64 on jenkins on '2024-11-21 01:55' Thu Nov 21 01:55:55 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/25892/console.log 1732154155 amd64 trixie rnahybrid Thu Nov 21 01:55:55 UTC 2024 I: Downloading source for trixie/rnahybrid=2.1.2-8 --2024-11-21 01:55:55-- http://deb.debian.org/debian/pool/main/r/rnahybrid/rnahybrid_2.1.2-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2315 (2.3K) [text/prs.lines.tag] Saving to: ‘rnahybrid_2.1.2-8.dsc’ 0K .. 100% 336M=0s 2024-11-21 01:55:55 (336 MB/s) - ‘rnahybrid_2.1.2-8.dsc’ saved [2315/2315] --2024-11-21 01:55:55-- http://deb.debian.org/debian/pool/main/r/rnahybrid/rnahybrid_2.1.2-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2315 (2.3K) [text/prs.lines.tag] Saving to: ‘rnahybrid_2.1.2-8.dsc’ 0K .. 100% 336M=0s 2024-11-21 01:55:55 (336 MB/s) - ‘rnahybrid_2.1.2-8.dsc’ saved [2315/2315] Thu Nov 21 01:55:55 UTC 2024 I: rnahybrid_2.1.2-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rnahybrid Binary: rnahybrid Architecture: any-amd64 any-i386 arm64 armhf loong64 mips mips64el mipsel ppc64el s390x alpha hppa m68k powerpc powerpcspe ppc64 sh4 sparc64 riscv64 Version: 2.1.2-8 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/submission.html Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/rnahybrid Vcs-Git: https://salsa.debian.org/med-team/rnahybrid.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libg2-dev Package-List: rnahybrid deb science optional arch=any-amd64,arm64,armhf,any-i386,loong64,mips,mips64el,mipsel,ppc64el,s390x,alpha,hppa,m68k,powerpc,powerpcspe,ppc64,sh4,sparc64,x32,riscv64 Checksums-Sha1: a5039de03c2b8d356e5d0c549613846d30934852 181984 rnahybrid_2.1.2.orig.tar.gz 0f3b73b3d6a67a590ec8f4f2041e97c2a85560cd 7184 rnahybrid_2.1.2-8.debian.tar.xz Checksums-Sha256: e2bbbca714441f709732412a1a130e4911e212419af5b09154ddfaf0148d6e96 181984 rnahybrid_2.1.2.orig.tar.gz 2836ef538bd5a320d3560659b6921b9d60ccd30eb072b40ce5e21a26fef06109 7184 rnahybrid_2.1.2-8.debian.tar.xz Files: 240f613f3fcc2f563f38804a54f07c89 181984 rnahybrid_2.1.2.orig.tar.gz dbd67b5622bd86233aff0542a4bb6655 7184 rnahybrid_2.1.2-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWEjUkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE+Gg/+PYDvPIZY8lH5Gfhwf6d3z9OZYeHeWBSA yHQ66cQjeCNQ4xctcUZ6nf09DjUOhJE17YleUHbG2Owm/5ZfUDnTQAtRuy9u+1z8 ar7sZJewDQFOXJr/3xcxjvV4yxhQ/tnk0kqZM7ISE6jpyhsARqZAfMSHFsf+5uai 3NHZUmLuZMyIIzdTGQJdmDAVetN3jpcu62HKS6onBoicUkLX08B/s//M+EUXVvP2 G/IcCakPxBGEtX16a93sgv8Br8jMCUc02YW0kTv57K275HXejs9xPvTqisUUMCpL uRwXYj6hClrPMrPsLb8wpEJNdXtBFSrHivPg1YLKBJkhbHjdwW4fRDu3ADYWEBtT g5EKGQspiDAuop1FiVLF7iYcD+NV7sSiFFwk+FG+PzKZ4v6j30yWqlfFA3Tb9iUp uGlwqpE1rROack+IYAHFWmvNk1Znpaxje0vYoxzn1ihzCUEemlZ9QwqUKWGNMD2D OwZL53jImD6dsM+vQ/tZJJfjknjAvCcEqp0ATXl6pYeJz9c5WjGJS/E0aju5q7df 8x8hCATJtoIIItM9cYgMpEl7AQ+L6Nfb98PcHDgMulf1jWSqOdvNBf24BSeNG6an 4brR317GM9yEQ/QDWtyDb+fgpJujyVsvMl+OWsCwRUZYZ2+iU8GlrmAbO1CCapFS VfpxCvKMwkU= =vB/g -----END PGP SIGNATURE----- Thu Nov 21 01:55:55 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 01:55:55 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Thu Nov 21 01:55:55 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Thu Nov 21 01:55:55 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Thu Nov 21 01:55:55 UTC 2024 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-7fPq9R' ==================================================================================== Thu Nov 21 01:55:56 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 rnahybrid trixie /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo 2.1.2-8" as arguments. Thu Nov 21 01:55:56 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-67dT9YiQ" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Nov 21 01:55:56 UTC 2024 I: Downloading source for trixie/rnahybrid=2.1.2-8 Reading package lists... NOTICE: 'rnahybrid' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rnahybrid.git Please use: git clone https://salsa.debian.org/med-team/rnahybrid.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 191 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (dsc) [2315 B] Get:2 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (tar) [182 kB] Get:3 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (diff) [7184 B] Fetched 191 kB in 0s (2229 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'rnahybrid' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rnahybrid.git Please use: git clone https://salsa.debian.org/med-team/rnahybrid.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 191 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (dsc) [2315 B] Get:2 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (tar) [182 kB] Get:3 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (diff) [7184 B] Fetched 191 kB in 0s (2229 kB/s) Download complete and in download only mode ============================================================================= Building rnahybrid in trixie on amd64 on ionos1-amd64 now. Date: Thu Nov 21 01:55:56 UTC 2024 Date UTC: Thu Nov 21 01:55:56 UTC 2024 ============================================================================= 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 Nov 20 13:55:57 -12 2024 I: pbuilder-time-stamp: 1732154157 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 [rnahybrid_2.1.2-8.dsc] I: copying [./rnahybrid_2.1.2.orig.tar.gz] I: copying [./rnahybrid_2.1.2-8.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 21 19:08:57 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rnahybrid_2.1.2-8.dsc: no acceptable signature found dpkg-source: info: extracting rnahybrid in rnahybrid-2.1.2 dpkg-source: info: unpacking rnahybrid_2.1.2.orig.tar.gz dpkg-source: info: unpacking rnahybrid_2.1.2-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fixmanpage.patch dpkg-source: info: applying mayhem_check_if_file_exists.patch dpkg-source: info: applying fix_loop_index.patch dpkg-source: info: applying fix_warnings.patch dpkg-source: info: applying fix-implicit-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4020306/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=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='91b9dcdf519c428ba45a96bd15b428de' 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='4020306' 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.QatqS3Oo/pbuilderrc_0EAZ --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.QatqS3Oo/b1 --logfile b1/build.log rnahybrid_2.1.2-8.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://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4020306/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), libg2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 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 libg2-dev; however: Package libg2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20230802{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbrotli1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libg2-dev{a} libg20{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpng16-16t64{a} libraqm0{a} librav1e0.7{a} libsharpyuv0{a} libsvtav1enc2{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxpm4{a} libyuv0{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 libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 35.5 MB of archives. After unpacking 122 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.11.0-1 [1879 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2+b2 [350 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 librav1e0.7 amd64 0.7.1-7+b2 [936 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc2 amd64 2.2.1+dfsg-2 [2173 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0.1888.20241107-1 [172 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 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 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.19.3-1 [11.2 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [15.0 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.19.3-1 [489 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libg20 amd64 0.72-12+b3 [41.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libg2-dev amd64 0.72-12+b3 [190 kB] Fetched 35.5 MB in 1s (47.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. 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Setting up libicu72:amd64 (72.1-5+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... No schema files found: doing nothing. Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libsvtav1enc2:amd64 (2.2.1+dfsg-2) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up libdav1d7:amd64 (1.5.0-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up librav1e0.7:amd64 (0.7.1-7+b2) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libabsl20230802:amd64 (20230802.1-4) ... Setting up libde265-0:amd64 (1.0.15-1+b2) ... Setting up libyuv0:amd64 (0.0.1888.20241107-1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libxpm4:amd64 (1:3.5.17-1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libgav1-1:amd64 (0.19.0-2+b2) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libavif16:amd64 (1.1.1-1) ... 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 libraqm0:amd64 (0.10.1-1+b2) ... Setting up debhelper (13.20) ... Setting up libheif-plugin-dav1d:amd64 (1.19.3-1) ... Setting up libheif1:amd64 (1.19.3-1) ... Setting up libgd3:amd64 (2.3.3-12+b1) ... Setting up libheif-plugin-libde265:amd64 (1.19.3-1) ... Setting up libg20 (0.72-12+b3) ... Setting up libg2-dev (0.72-12+b3) ... Processing triggers for libc-bin (2.40-3) ... 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/rnahybrid-2.1.2/ && 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 > ../rnahybrid_2.1.2-8_source.changes dpkg-buildpackage: info: source package rnahybrid dpkg-buildpackage: info: source version 2.1.2-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:8: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.in:8: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:745: AM_CONFIG_HEADER is expanded from... configure.in:8: the top level configure.in:21: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:21: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:21: the top level configure.in:34: warning: AC_OUTPUT should be used without arguments. configure.in:34: You should run autoupdate. autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:12: installing './compile' src/Makefile.am:62: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for log in -lm... yes checking for g2_open_vd in -lg2... yes checking for gdImageLine in -lgd... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for g2.h... yes checking for g2_PS.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j20 make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make all-recursive make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' Making all in src make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnahybrid.o rnahybrid.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o hybrid_core.o hybrid_core.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o energy.o energy.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o input.o input.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o fasta.o fasta.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o plot.o plot.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnacalibrate.o rnacalibrate.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o numerical.o numerical.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o random.o random.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o mt19937-1.o mt19937-1.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnaeffective.o rnaeffective.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAhybrid rnahybrid.o hybrid_core.o energy.o input.o fasta.o plot.o -lg2 -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAcalibrate rnacalibrate.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o -lg2 -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAeffective rnaeffective.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o -lg2 -lm make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' Making all in man make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' src/RNAhybrid -s 3utr_worm -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -28.2 kcal/mol p-value: 0.064406 position 1265 target 5' U GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAcalibrate -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta cel-let-7 17 1.984979 0.251514 src/RNAhybrid -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -28.2 kcal/mol p-value: 0.052460 position 1265 target 5' U GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAhybrid -f 2,7 -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -27.3 kcal/mol p-value: 0.070821 position 1189 target 5' C AU U C 3' CUGUAUA GCCU CUACCUC GAUAUGU UGGA GAUGGAG miRNA 3' UU U U 5' src/RNAcalibrate -f 2,7 -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta cel-let-7 13 1.250098 0.436537 src/RNAhybrid -s 3utr_worm -t examples/cbr-hbl-1.fasta -q examples/cel-let-7.fasta target: ENSCBRT00000006770.1|ENSCBRG00000005546.1 length: 1449 miRNA : cel-let-7 length: 22 mfe: -28.3 kcal/mol p-value: 0.060792 position 1333 target 5' C GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAeffective -k 30 -s -t examples/hbl-1.fasta -q examples/cel-let-7.fasta 1.000000 0.410085 1.100000 0.225971 1.200000 0.202579 1.300000 0.277040 1.400000 0.423521 1.500000 0.753856 1.600000 1.098540 1.700000 1.546734 1.800000 1.952964 1.900000 2.538049 2.000000 3.157561 Effective number: 1.200000 make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rnahybrid/ make -j20 install DESTDIR=/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' Making install in src make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' /usr/bin/install -c RNAhybrid RNAcalibrate RNAeffective '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' Making install in man make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/share/man/man1' /usr/bin/install -c -m 644 RNAhybrid.1 RNAcalibrate.1 RNAeffective.1 '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rnahybrid-dbgsym' in '../rnahybrid-dbgsym_2.1.2-8_amd64.deb'. dpkg-deb: building package 'rnahybrid' in '../rnahybrid_2.1.2-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rnahybrid_2.1.2-8_amd64.buildinfo dpkg-genchanges --build=binary -O../rnahybrid_2.1.2-8_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/4020306 and its subdirectories I: Current time: Wed Nov 20 13:58:25 -12 2024 I: pbuilder-time-stamp: 1732154305 Thu Nov 21 01:58:25 UTC 2024 I: Signing ./b1/rnahybrid_2.1.2-8_amd64.buildinfo as rnahybrid_2.1.2-8_amd64.buildinfo.asc Thu Nov 21 01:58:25 UTC 2024 I: Signed ./b1/rnahybrid_2.1.2-8_amd64.buildinfo as ./b1/rnahybrid_2.1.2-8_amd64.buildinfo.asc Thu Nov 21 01:58:25 UTC 2024 - build #1 for rnahybrid/trixie/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Thu Nov 21 01:58:25 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-67dT9YiQ, removing. /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 01:58 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 01:55 b2 -rw------- 1 jenkins jenkins 3425 Nov 21 01:55 rbuildlog.R9d1MIP -rw-r--r-- 1 jenkins jenkins 2315 Dec 21 2023 rnahybrid_2.1.2-8.dsc /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b1: total 464 -rw-r--r-- 1 jenkins jenkins 47418 Nov 21 01:58 build.log -rw-r--r-- 1 jenkins jenkins 218220 Nov 21 01:58 rnahybrid-dbgsym_2.1.2-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 7184 Nov 21 01:58 rnahybrid_2.1.2-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2315 Nov 21 01:58 rnahybrid_2.1.2-8.dsc -rw-r--r-- 1 jenkins jenkins 6241 Nov 21 01:58 rnahybrid_2.1.2-8_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7123 Nov 21 01:58 rnahybrid_2.1.2-8_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1393 Nov 21 01:58 rnahybrid_2.1.2-8_amd64.changes -rw-r--r-- 1 jenkins jenkins 163900 Nov 21 01:58 rnahybrid_2.1.2-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 1237 Nov 21 01:58 rnahybrid_2.1.2-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b2: total 0 Thu Nov 21 01:58:25 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Nov 20 13:55:57 -12 2024 I: pbuilder-time-stamp: 1732154157 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 [rnahybrid_2.1.2-8.dsc] I: copying [./rnahybrid_2.1.2.orig.tar.gz] I: copying [./rnahybrid_2.1.2-8.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 21 19:08:57 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rnahybrid_2.1.2-8.dsc: no acceptable signature found dpkg-source: info: extracting rnahybrid in rnahybrid-2.1.2 dpkg-source: info: unpacking rnahybrid_2.1.2.orig.tar.gz dpkg-source: info: unpacking rnahybrid_2.1.2-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fixmanpage.patch dpkg-source: info: applying mayhem_check_if_file_exists.patch dpkg-source: info: applying fix_loop_index.patch dpkg-source: info: applying fix_warnings.patch dpkg-source: info: applying fix-implicit-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4020306/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=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='91b9dcdf519c428ba45a96bd15b428de' 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='4020306' 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.QatqS3Oo/pbuilderrc_0EAZ --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.QatqS3Oo/b1 --logfile b1/build.log rnahybrid_2.1.2-8.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://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4020306/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), libg2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 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 libg2-dev; however: Package libg2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20230802{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbrotli1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libg2-dev{a} libg20{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpng16-16t64{a} libraqm0{a} librav1e0.7{a} libsharpyuv0{a} libsvtav1enc2{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxpm4{a} libyuv0{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 libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 35.5 MB of archives. After unpacking 122 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.11.0-1 [1879 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2+b2 [350 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 librav1e0.7 amd64 0.7.1-7+b2 [936 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc2 amd64 2.2.1+dfsg-2 [2173 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0.1888.20241107-1 [172 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 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 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.19.3-1 [11.2 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [15.0 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.19.3-1 [489 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libg20 amd64 0.72-12+b3 [41.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libg2-dev amd64 0.72-12+b3 [190 kB] Fetched 35.5 MB in 1s (47.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... 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_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../29-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../30-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../31-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libabsl20230802:amd64. Preparing to unpack .../32-libabsl20230802_20230802.1-4_amd64.deb ... 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Processing triggers for libc-bin (2.40-3) ... 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/rnahybrid-2.1.2/ && 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 > ../rnahybrid_2.1.2-8_source.changes dpkg-buildpackage: info: source package rnahybrid dpkg-buildpackage: info: source version 2.1.2-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:8: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.in:8: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:745: AM_CONFIG_HEADER is expanded from... configure.in:8: the top level configure.in:21: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:21: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:21: the top level configure.in:34: warning: AC_OUTPUT should be used without arguments. configure.in:34: You should run autoupdate. autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:12: installing './compile' src/Makefile.am:62: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for log in -lm... yes checking for g2_open_vd in -lg2... yes checking for gdImageLine in -lgd... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for g2.h... yes checking for g2_PS.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j20 make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make all-recursive make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' Making all in src make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnahybrid.o rnahybrid.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o hybrid_core.o hybrid_core.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o energy.o energy.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o input.o input.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o fasta.o fasta.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o plot.o plot.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnacalibrate.o rnacalibrate.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o numerical.o numerical.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o random.o random.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o mt19937-1.o mt19937-1.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnaeffective.o rnaeffective.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAhybrid rnahybrid.o hybrid_core.o energy.o input.o fasta.o plot.o -lg2 -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAcalibrate rnacalibrate.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o -lg2 -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAeffective rnaeffective.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o -lg2 -lm make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' Making all in man make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' src/RNAhybrid -s 3utr_worm -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -28.2 kcal/mol p-value: 0.064406 position 1265 target 5' U GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAcalibrate -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta cel-let-7 17 1.984979 0.251514 src/RNAhybrid -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -28.2 kcal/mol p-value: 0.052460 position 1265 target 5' U GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAhybrid -f 2,7 -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -27.3 kcal/mol p-value: 0.070821 position 1189 target 5' C AU U C 3' CUGUAUA GCCU CUACCUC GAUAUGU UGGA GAUGGAG miRNA 3' UU U U 5' src/RNAcalibrate -f 2,7 -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta cel-let-7 13 1.250098 0.436537 src/RNAhybrid -s 3utr_worm -t examples/cbr-hbl-1.fasta -q examples/cel-let-7.fasta target: ENSCBRT00000006770.1|ENSCBRG00000005546.1 length: 1449 miRNA : cel-let-7 length: 22 mfe: -28.3 kcal/mol p-value: 0.060792 position 1333 target 5' C GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAeffective -k 30 -s -t examples/hbl-1.fasta -q examples/cel-let-7.fasta 1.000000 0.410085 1.100000 0.225971 1.200000 0.202579 1.300000 0.277040 1.400000 0.423521 1.500000 0.753856 1.600000 1.098540 1.700000 1.546734 1.800000 1.952964 1.900000 2.538049 2.000000 3.157561 Effective number: 1.200000 make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rnahybrid/ make -j20 install DESTDIR=/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' Making install in src make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' /usr/bin/install -c RNAhybrid RNAcalibrate RNAeffective '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' Making install in man make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/share/man/man1' /usr/bin/install -c -m 644 RNAhybrid.1 RNAcalibrate.1 RNAeffective.1 '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rnahybrid-dbgsym' in '../rnahybrid-dbgsym_2.1.2-8_amd64.deb'. dpkg-deb: building package 'rnahybrid' in '../rnahybrid_2.1.2-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rnahybrid_2.1.2-8_amd64.buildinfo dpkg-genchanges --build=binary -O../rnahybrid_2.1.2-8_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/4020306 and its subdirectories I: Current time: Wed Nov 20 13:58:25 -12 2024 I: pbuilder-time-stamp: 1732154305 Thu Nov 21 01:58:26 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Thu Nov 21 01:58:26 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Thu Nov 21 01:58:26 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Thu Nov 21 01:58:26 UTC 2024 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-duzWWz' ==================================================================================== Wed Dec 24 08:21:48 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 rnahybrid trixie /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo 2.1.2-8" as arguments. Wed Dec 24 08:21:49 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-oYq2WrcI" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Dec 24 08:21:49 UTC 2025 I: Downloading source for trixie/rnahybrid=2.1.2-8 Reading package lists... NOTICE: 'rnahybrid' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rnahybrid.git Please use: git clone https://salsa.debian.org/med-team/rnahybrid.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 191 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (dsc) [2315 B] Get:2 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (tar) [182 kB] Get:3 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (diff) [7184 B] Fetched 191 kB in 0s (8445 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'rnahybrid' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/rnahybrid.git Please use: git clone https://salsa.debian.org/med-team/rnahybrid.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 191 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (dsc) [2315 B] Get:2 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (tar) [182 kB] Get:3 http://deb.debian.org/debian trixie/main rnahybrid 2.1.2-8 (diff) [7184 B] Fetched 191 kB in 0s (8445 kB/s) Download complete and in download only mode ============================================================================= Re-Building rnahybrid in trixie on amd64 on ionos15-amd64 now. Date: Wed Dec 24 08:21:52 UTC 2025 Date UTC: Wed Dec 24 08:21:52 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/pbuilderrc_5rdc + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' rnahybrid = debian-installer -o rnahybrid = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' rnahybrid = u-boot ']' + case "${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.QatqS3Oo/pbuilderrc_5rdc --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b2 --logfile b2/build.log rnahybrid_2.1.2-8.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: Wed Dec 24 22:21:52 +14 2025 I: pbuilder-time-stamp: 1766564512 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 [rnahybrid_2.1.2-8.dsc] I: copying [./rnahybrid_2.1.2.orig.tar.gz] I: copying [./rnahybrid_2.1.2-8.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 21 19:08:57 2023 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rnahybrid_2.1.2-8.dsc: no acceptable signature found dpkg-source: info: extracting rnahybrid in rnahybrid-2.1.2 dpkg-source: info: unpacking rnahybrid_2.1.2.orig.tar.gz dpkg-source: info: unpacking rnahybrid_2.1.2-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc-4.8.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying fixmanpage.patch dpkg-source: info: applying mayhem_check_if_file_exists.patch dpkg-source: info: applying fix_loop_index.patch dpkg-source: info: applying fix_warnings.patch dpkg-source: info: applying fix-implicit-declaration.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2568511/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-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 Dec 24 08:25 /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/2568511/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2568511/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=eb71eaaa99294a148c8777f7152c93df 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=2568511 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.QatqS3Oo/pbuilderrc_5rdc --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b2 --logfile b2/build.log rnahybrid_2.1.2-8.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2568511/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), libg2-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19969 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 libg2-dev; however: Package libg2-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20230802{a} libaom3{a} libarchive-zip-perl{a} libavif16{a} libbrotli1{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libg2-dev{a} libg20{a} libgav1-1{a} libgd3{a} libglib2.0-0t64{a} libgraphite2-3{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpng16-16t64{a} libraqm0{a} librav1e0.7{a} libsharpyuv0{a} libsvtav1enc2{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxpm4{a} libyuv0{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 libglib2.0-data libheif-plugin-aomenc libheif-plugin-x265 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 35.5 MB of archives. After unpacking 122 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libaom3 amd64 3.11.0-1 [1879 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libgav1-1 amd64 0.19.0-2+b2 [350 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 librav1e0.7 amd64 0.7.1-7+b2 [936 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libsvtav1enc2 amd64 2.2.1+dfsg-2 [2173 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libyuv0 amd64 0.0.1888.20241107-1 [172 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 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 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-dav1d amd64 1.19.3-1 [11.2 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [15.0 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libheif1 amd64 1.19.3-1 [489 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libg20 amd64 0.72-12+b3 [41.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libg2-dev amd64 0.72-12+b3 [190 kB] Fetched 35.5 MB in 7s (5172 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_amd64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-11_amd64.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:amd64. 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Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.22.5-2_amd64.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-intltool-debian_0.35.0+20060710.6_all.deb ... 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_13.20_all.deb ... Unpacking debhelper (13.20) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../29-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../30-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../31-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libabsl20230802:amd64. Preparing to unpack .../32-libabsl20230802_20230802.1-4_amd64.deb ... Unpacking libabsl20230802:amd64 (20230802.1-4) ... Selecting previously unselected package libaom3:amd64. Preparing to unpack .../33-libaom3_3.11.0-1_amd64.deb ... Unpacking libaom3:amd64 (3.11.0-1) ... Selecting previously unselected package libdav1d7:amd64. Preparing to unpack .../34-libdav1d7_1.5.0-1+b1_amd64.deb ... Unpacking libdav1d7:amd64 (1.5.0-1+b1) ... Selecting previously unselected package libgav1-1:amd64. Preparing to unpack .../35-libgav1-1_0.19.0-2+b2_amd64.deb ... Unpacking libgav1-1:amd64 (0.19.0-2+b2) ... Selecting previously unselected package librav1e0.7:amd64. Preparing to unpack .../36-librav1e0.7_0.7.1-7+b2_amd64.deb ... Unpacking librav1e0.7:amd64 (0.7.1-7+b2) ... Selecting previously unselected package libsvtav1enc2:amd64. Preparing to unpack .../37-libsvtav1enc2_2.2.1+dfsg-2_amd64.deb ... Unpacking libsvtav1enc2:amd64 (2.2.1+dfsg-2) ... Selecting previously unselected package libjpeg62-turbo:amd64. 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Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../44-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../45-libpng16-16t64_1.6.44-2_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../46-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../47-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../48-libfribidi0_1.0.15-1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.15-1) ... Selecting previously unselected package libsharpyuv0:amd64. Preparing to unpack .../49-libsharpyuv0_1.4.0-0.1+b1_amd64.deb ... Unpacking libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Selecting previously unselected package libheif-plugin-dav1d:amd64. Preparing to unpack .../50-libheif-plugin-dav1d_1.19.3-1_amd64.deb ... Unpacking libheif-plugin-dav1d:amd64 (1.19.3-1) ... Selecting previously unselected package libheif-plugin-libde265:amd64. Preparing to unpack .../51-libheif-plugin-libde265_1.19.3-1_amd64.deb ... Unpacking libheif-plugin-libde265:amd64 (1.19.3-1) ... Selecting previously unselected package libheif1:amd64. Preparing to unpack .../52-libheif1_1.19.3-1_amd64.deb ... Unpacking libheif1:amd64 (1.19.3-1) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../53-libimagequant0_2.18.0-1+b2_amd64.deb ... Unpacking libimagequant0:amd64 (2.18.0-1+b2) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../54-libglib2.0-0t64_2.82.2-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-2) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../55-libgraphite2-3_1.3.14-2+b1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-2+b1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../56-libharfbuzz0b_10.0.1-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (10.0.1-1) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../57-libraqm0_0.10.1-1+b2_amd64.deb ... Unpacking libraqm0:amd64 (0.10.1-1+b2) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../58-libjbig0_2.1-6.1+b2_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1+b2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../59-liblerc4_4.0.0+ds-5_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-5) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../60-libwebp7_1.4.0-0.1+b1_amd64.deb ... Unpacking libwebp7:amd64 (1.4.0-0.1+b1) ... 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Processing triggers for libc-bin (2.40-3) ... 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: user script /srv/workspace/pbuilder/2568511/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2568511/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/rnahybrid-2.1.2/ && 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 > ../rnahybrid_2.1.2-8_source.changes dpkg-buildpackage: info: source package rnahybrid dpkg-buildpackage: info: source version 2.1.2-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:8: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.in:8: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:745: AM_CONFIG_HEADER is expanded from... configure.in:8: the top level configure.in:21: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:21: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:21: the top level configure.in:34: warning: AC_OUTPUT should be used without arguments. configure.in:34: You should run autoupdate. autoheader: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:12: installing './compile' src/Makefile.am:62: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking for log in -lm... yes checking for g2_open_vd in -lg2... yes checking for gdImageLine in -lgd... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for g2.h... yes checking for g2_PS.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make all-recursive make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' Making all in src make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnahybrid.o rnahybrid.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o hybrid_core.o hybrid_core.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o energy.o energy.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o input.o input.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o fasta.o fasta.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o plot.o plot.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnacalibrate.o rnacalibrate.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o numerical.o numerical.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o random.o random.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o mt19937-1.o mt19937-1.c gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -c -o rnaeffective.o rnaeffective.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAhybrid rnahybrid.o hybrid_core.o energy.o input.o fasta.o plot.o -lg2 -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAcalibrate rnacalibrate.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o -lg2 -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fcommon -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAeffective rnaeffective.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o -lg2 -lm make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' Making all in man make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' src/RNAhybrid -s 3utr_worm -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -28.2 kcal/mol p-value: 0.064406 position 1265 target 5' U GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAcalibrate -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta cel-let-7 16 2.055099 0.214185 src/RNAhybrid -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -28.2 kcal/mol p-value: 0.052460 position 1265 target 5' U GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAhybrid -f 2,7 -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 miRNA : cel-let-7 length: 22 mfe: -27.3 kcal/mol p-value: 0.070821 position 1189 target 5' C AU U C 3' CUGUAUA GCCU CUACCUC GAUAUGU UGGA GAUGGAG miRNA 3' UU U U 5' src/RNAcalibrate -f 2,7 -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta cel-let-7 14 1.048324 0.423273 src/RNAhybrid -s 3utr_worm -t examples/cbr-hbl-1.fasta -q examples/cel-let-7.fasta target: ENSCBRT00000006770.1|ENSCBRG00000005546.1 length: 1449 miRNA : cel-let-7 length: 22 mfe: -28.3 kcal/mol p-value: 0.060792 position 1333 target 5' C GUU C A 3' AUUAUACAACC C ACCUCA UGAUAUGUUGG G UGGAGU miRNA 3' U AU A 5' src/RNAeffective -k 30 -s -t examples/hbl-1.fasta -q examples/cel-let-7.fasta 1.000000 0.586835 1.100000 0.465475 1.200000 0.425465 1.300000 0.571329 1.400000 0.734830 1.500000 0.930651 1.600000 1.342548 1.700000 1.858599 1.800000 2.008570 1.900000 2.633853 2.000000 3.270614 Effective number: 1.200000 make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rnahybrid/ make -j42 install DESTDIR=/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' Making install in src make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' /usr/bin/install -c RNAhybrid RNAcalibrate RNAeffective '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/src' Making install in man make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/share/man/man1' /usr/bin/install -c -m 644 RNAhybrid.1 RNAcalibrate.1 RNAeffective.1 '/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2/man' make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[2]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'rnahybrid' in '../rnahybrid_2.1.2-8_amd64.deb'. dpkg-deb: building package 'rnahybrid-dbgsym' in '../rnahybrid-dbgsym_2.1.2-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rnahybrid_2.1.2-8_amd64.buildinfo dpkg-genchanges --build=binary -O../rnahybrid_2.1.2-8_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/2568511/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2568511/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/2568511 and its subdirectories I: Current time: Wed Dec 24 22:30:34 +14 2025 I: pbuilder-time-stamp: 1766565034 + false + set +x Wed Dec 24 08:30:34 UTC 2025 I: Signing ./b2/rnahybrid_2.1.2-8_amd64.buildinfo as rnahybrid_2.1.2-8_amd64.buildinfo.asc Wed Dec 24 08:30:34 UTC 2025 I: Signed ./b2/rnahybrid_2.1.2-8_amd64.buildinfo as ./b2/rnahybrid_2.1.2-8_amd64.buildinfo.asc Wed Dec 24 08:30:34 UTC 2025 - build #2 for rnahybrid/trixie/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Wed Dec 24 08:30:34 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-oYq2WrcI, removing. /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo: total 68 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 01:58 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 21 02:07 b2 -rw------- 1 jenkins jenkins 51131 Nov 21 01:58 rbuildlog.R9d1MIP -rw-r--r-- 1 jenkins jenkins 2315 Dec 21 2023 rnahybrid_2.1.2-8.dsc /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b1: total 472 -rw-r--r-- 1 jenkins jenkins 47418 Nov 21 01:58 build.log -rw-r--r-- 1 jenkins jenkins 218220 Nov 21 01:58 rnahybrid-dbgsym_2.1.2-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 7184 Nov 21 01:58 rnahybrid_2.1.2-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2315 Nov 21 01:58 rnahybrid_2.1.2-8.dsc -rw-r--r-- 1 jenkins jenkins 6241 Nov 21 01:58 rnahybrid_2.1.2-8_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7123 Nov 21 01:58 rnahybrid_2.1.2-8_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1393 Nov 21 01:58 rnahybrid_2.1.2-8_amd64.changes -rw-r--r-- 1 jenkins jenkins 163900 Nov 21 01:58 rnahybrid_2.1.2-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 1237 Nov 21 01:58 rnahybrid_2.1.2-8_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b2: total 468 -rw-r--r-- 1 jenkins jenkins 49360 Nov 21 02:07 build.log -rw-r--r-- 1 jenkins jenkins 218220 Nov 21 02:07 rnahybrid-dbgsym_2.1.2-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 7184 Nov 21 02:07 rnahybrid_2.1.2-8.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2315 Nov 21 02:07 rnahybrid_2.1.2-8.dsc -rw-r--r-- 1 jenkins jenkins 6250 Nov 21 02:07 rnahybrid_2.1.2-8_amd64.buildinfo -rw-r--r-- 1 jenkins jenkins 7132 Nov 21 02:07 rnahybrid_2.1.2-8_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1393 Nov 21 02:07 rnahybrid_2.1.2-8_amd64.changes -rw-r--r-- 1 jenkins jenkins 163900 Nov 21 02:07 rnahybrid_2.1.2-8_amd64.deb -rw-r--r-- 1 jenkins jenkins 1237 Nov 21 02:07 rnahybrid_2.1.2-8_source.changes Thu Nov 21 02:07:35 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Thu Nov 21 02:07:36 UTC 2024 I: rnahybrid_2.1.2-8_amd64.changes: Format: 1.8 Date: Thu, 21 Dec 2023 19:49:33 +0100 Source: rnahybrid Binary: rnahybrid rnahybrid-dbgsym Architecture: amd64 Version: 2.1.2-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: rnahybrid - Fast and effective prediction of microRNA/target duplexes Closes: 1058990 Changes: rnahybrid (2.1.2-8) unstable; urgency=medium . * Add build support for loongarch64 Closes: #1058990 Checksums-Sha1: 7a290d52c4f914a9d737080ae1f81164765c8767 218220 rnahybrid-dbgsym_2.1.2-8_amd64.deb 6ebae38223147247dbae3c86a13038406eb81fcc 6241 rnahybrid_2.1.2-8_amd64.buildinfo f587d9c357d4db090ed999c34e428c8f29f21353 163900 rnahybrid_2.1.2-8_amd64.deb Checksums-Sha256: ab2d838ef04a374899a4678ac4c0d0abc7f6b058ec38bddac673ba8e58e98071 218220 rnahybrid-dbgsym_2.1.2-8_amd64.deb e4cc16f7a48be0f2902a009629d2337257e500b5f857f3d8a781866de7691507 6241 rnahybrid_2.1.2-8_amd64.buildinfo 6699924f27921e5fa3f49c2f6d43b057adcdafaff9e56bb198408fcd9cdf2f44 163900 rnahybrid_2.1.2-8_amd64.deb Files: 4dc1603446106081d7e41a0e57c13e82 218220 debug optional rnahybrid-dbgsym_2.1.2-8_amd64.deb ea9f9ea0aad2c384e23da3325fc26831 6241 science optional rnahybrid_2.1.2-8_amd64.buildinfo 8a461db64578f5258f4fa8ca98825278 163900 science optional rnahybrid_2.1.2-8_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/rnahybrid_2.1.2-8.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/rnahybrid_2.1.2-8.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/rnahybrid_2.1.2-8.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/amd64/rnahybrid_2.1.2-8.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/amd64/rnahybrid_2.1.2-8_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/rnahybrid_2.1.2-8.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-21 01:58:25.703012834 +0000 +++ b2/build.log 2024-11-21 02:07:35.626163345 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Nov 20 13:55:57 -12 2024 -I: pbuilder-time-stamp: 1732154157 +I: Current time: Wed Dec 24 22:21:52 +14 2025 +I: pbuilder-time-stamp: 1766564512 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying fix-implicit-declaration.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/4020306/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2568511/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Dec 24 08:25 /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/2568511/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2568511/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=20 ' - DISTRIBUTION='trixie' - 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]="2" [2]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='91b9dcdf519c428ba45a96bd15b428de' - 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='4020306' - PS1='# ' - PS2='> ' + INVOCATION_ID=eb71eaaa99294a148c8777f7152c93df + 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=2568511 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.QatqS3Oo/pbuilderrc_0EAZ --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.QatqS3Oo/b1 --logfile b1/build.log rnahybrid_2.1.2-8.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://46.16.76.132:3128' + 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.QatqS3Oo/pbuilderrc_5rdc --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b2 --logfile b2/build.log rnahybrid_2.1.2-8.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4020306/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2568511/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -188,7 +220,7 @@ Get: 69 http://deb.debian.org/debian trixie/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libg20 amd64 0.72-12+b3 [41.5 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libg2-dev amd64 0.72-12+b3 [190 kB] -Fetched 35.5 MB in 1s (47.8 MB/s) +Fetched 35.5 MB in 7s (5172 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19969 files and directories currently installed.) @@ -488,7 +520,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rnahybrid-2.1.2/ && 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 > ../rnahybrid_2.1.2-8_source.changes +I: user script /srv/workspace/pbuilder/2568511/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2568511/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rnahybrid-2.1.2/ && 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 > ../rnahybrid_2.1.2-8_source.changes dpkg-buildpackage: info: source package rnahybrid dpkg-buildpackage: info: source version 2.1.2-8 dpkg-buildpackage: info: source distribution unstable @@ -568,7 +604,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j20 + make -j42 make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' make all-recursive make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' @@ -616,7 +652,7 @@ src/RNAcalibrate -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta -cel-let-7 17 1.984979 0.251514 +cel-let-7 16 2.055099 0.214185 src/RNAhybrid -d 1.9,0.28 -t examples/cel-hbl-1.fasta -q examples/cel-let-7.fasta target: F13D11.2.1|F13D11.2.1 length: 1458 @@ -650,7 +686,7 @@ src/RNAcalibrate -f 2,7 -d examples/3UTR_worm.freq -k 50 -l 50,30 -q examples/cel-let-7.fasta -cel-let-7 13 1.250098 0.436537 +cel-let-7 14 1.048324 0.423273 src/RNAhybrid -s 3utr_worm -t examples/cbr-hbl-1.fasta -q examples/cel-let-7.fasta target: ENSCBRT00000006770.1|ENSCBRG00000005546.1 length: 1449 @@ -668,23 +704,23 @@ src/RNAeffective -k 30 -s -t examples/hbl-1.fasta -q examples/cel-let-7.fasta -1.000000 0.410085 -1.100000 0.225971 -1.200000 0.202579 -1.300000 0.277040 -1.400000 0.423521 -1.500000 0.753856 -1.600000 1.098540 -1.700000 1.546734 -1.800000 1.952964 -1.900000 2.538049 -2.000000 3.157561 +1.000000 0.586835 +1.100000 0.465475 +1.200000 0.425465 +1.300000 0.571329 +1.400000 0.734830 +1.500000 0.930651 +1.600000 1.342548 +1.700000 1.858599 +1.800000 2.008570 +1.900000 2.633853 +2.000000 3.270614 Effective number: 1.200000 make[1]: Leaving directory '/build/reproducible-path/rnahybrid-2.1.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rnahybrid/ - make -j20 install DESTDIR=/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid AM_UPDATE_INFO_DIR=no + make -j42 install DESTDIR=/build/reproducible-path/rnahybrid-2.1.2/debian/rnahybrid AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2' Making install in src make[2]: Entering directory '/build/reproducible-path/rnahybrid-2.1.2/src' @@ -727,8 +763,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'rnahybrid-dbgsym' in '../rnahybrid-dbgsym_2.1.2-8_amd64.deb'. dpkg-deb: building package 'rnahybrid' in '../rnahybrid_2.1.2-8_amd64.deb'. +dpkg-deb: building package 'rnahybrid-dbgsym' in '../rnahybrid-dbgsym_2.1.2-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rnahybrid_2.1.2-8_amd64.buildinfo dpkg-genchanges --build=binary -O../rnahybrid_2.1.2-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -736,12 +772,14 @@ 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/2568511/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2568511/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/4020306 and its subdirectories -I: Current time: Wed Nov 20 13:58:25 -12 2024 -I: pbuilder-time-stamp: 1732154305 +I: removing directory /srv/workspace/pbuilder/2568511 and its subdirectories +I: Current time: Wed Dec 24 22:30:34 +14 2025 +I: pbuilder-time-stamp: 1766565034 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/rnahybrid_2.1.2-8.diff: 67.1% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/amd64/rnahybrid_2.1.2-8.diff.gz b2/build.log: 80.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 80.6% -- replaced with stdout Thu Nov 21 02:07:37 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_rnahybrid_trixie_amd64_1732154857 + touch /var/log/reproducible-builds/diffoscope_stamp_rnahybrid_trixie_amd64_1732154857 + RESULT=0 + systemd-run '--description=diffoscope on rnahybrid/2.1.2-8 in trixie/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_29-25892 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo --run-session -c jenkins-reproducible-trixie-diffoscope-1c78c9e5-d428-4670-a5ba-35bf1db34dad -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/dbd-tmp-HXnWkuw ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/rnahybrid_2.1.2-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/rnahybrid_2.1.2-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/rnahybrid_2.1.2-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b1/rnahybrid_2.1.2-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b2/rnahybrid_2.1.2-8_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_29-25892.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/rnahybrid_2.1.2-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/rnahybrid_2.1.2-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/rnahybrid_2.1.2-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b1/rnahybrid_2.1.2-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.QatqS3Oo/b2/rnahybrid_2.1.2-8_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 abc.DotChangesFile ## main (total time: 0.348s) 0.348s 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: 660ms CPU time consumed: 653ms _ _ _ _ _ __ _ __ __ _| |__ _ _| |__ _ __(_) __| | | '__| '_ \ / _` | '_ \| | | | '_ \| '__| |/ _` | | | | | | | (_| | | | | |_| | |_) | | | | (_| | |_| |_| |_|\__,_|_| |_|\__, |_.__/|_| |_|\__,_| |___/ Thu Nov 21 02:07:38 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 02:07:38 UTC 2024 I: rnahybrid from trixie built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-21 02:07:38] INFO: Starting at 2024-11-21 02:07:38.905565 [2024-11-21 02:07:38] INFO: Generating the pages of 1 package(s) [2024-11-21 02:07:39] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/amd64/rnahybrid didn't produce a buildlog, even though it has been built. [2024-11-21 02:07:39] INFO: Finished at 2024-11-21 02:07:39.348037, took: 0:00:00.442481 Thu Nov 21 02:07:39 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/amd64/rnahybrid.html Thu Nov 21 02:07:39 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 02:07:39 UTC 2024 I: Submitting 8.0K b1/rnahybrid_2.1.2-8_amd64.buildinfo.asc https://buildinfo.debian.net/6ebae38223147247dbae3c86a13038406eb81fcc/rnahybrid_2.1.2-8_amd64 Thu Nov 21 02:07:40 UTC 2024 I: Submitting 8.0K b2/rnahybrid_2.1.2-8_amd64.buildinfo.asc https://buildinfo.debian.net/5aa3ba8347ccedd853f6f6449e5d7ce8f891c51e/rnahybrid_2.1.2-8_amd64 Thu Nov 21 02:07:41 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 02:07:41 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 02:07:41 UTC 2024 I: Removing signed rnahybrid_2.1.2-8_amd64.buildinfo.asc files: removed './b1/rnahybrid_2.1.2-8_amd64.buildinfo.asc' removed './b2/rnahybrid_2.1.2-8_amd64.buildinfo.asc' 1732154861 amd64 trixie rnahybrid Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/rnahybrid_2.1.2-8.rbuild.log: 77.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/amd64/rnahybrid_2.1.2-8.rbuild.log.gz [2024-11-21 02:07:41] INFO: Starting at 2024-11-21 02:07:41.731696 [2024-11-21 02:07:41] INFO: Generating the pages of 1 package(s) [2024-11-21 02:07:42] INFO: Finished at 2024-11-21 02:07:42.206761, took: 0:00:00.475073 All cleanup done. Thu Nov 21 02:07:42 UTC 2024 - total duration: 0h 11m 55s. Thu Nov 21 02:07:42 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-2m4tqreU, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 11min 59.125s CPU time consumed: 7.284s