Wed May 8 08:21:19 UTC 2024 I: starting to build rnahybrid/trixie/i386 on jenkins on '2024-05-08 08:20' Wed May 8 08:21:19 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_10/11021/console.log Wed May 8 08:21:19 UTC 2024 I: Downloading source for trixie/rnahybrid=2.1.2-8 --2024-05-08 08:21:19-- 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% 309M=0s 2024-05-08 08:21:19 (309 MB/s) - ‘rnahybrid_2.1.2-8.dsc’ saved [2315/2315] Wed May 8 08:21:19 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----- Wed May 8 08:21:19 UTC 2024 I: Checking whether the package is not for us Wed May 8 08:21:19 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Wed May 8 08:21:19 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Wed May 8 08:23:39 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 10 02:44:22 -12 2025 I: pbuilder-time-stamp: 1749566662 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: using eatmydata during job 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/31867/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='6f578ec608d3493688421c8d4195e9bc' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='31867' 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.A9yYrUPS/pbuilderrc_K436 --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.A9yYrUPS/b1 --logfile b1/build.log rnahybrid_2.1.2-8.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos16-i386 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 8 17:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/31867/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: i386 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 ... 19683 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} libbsd0{a} libdav1d7{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libg2-dev{a} libg20{a} libgav1-1{a} libgd3{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpng16-16t64{a} librav1e0{a} libsharpyuv0{a} libsub-override-perl{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 libheif-plugin-aomenc libheif-plugin-x265 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 30.1 MB of archives. After unpacking 105 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3 [114 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.21-14+b1 [162 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b1 [69.1 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-4 [1194 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40-8 [97.2 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.7-2 [39.7 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 man-db i386 2.12.1-1 [1421 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.191-1+b1 [194 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-4+b1 [9549 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.9.14+dfsg-1.3+b3 [727 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 gettext i386 0.21-14+b1 [1311 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 fontconfig-config i386 2.15.0-1.1 [317 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libabsl20230802 i386 20230802.1-4 [521 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libaom3 i386 3.8.2-2 [1910 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libdav1d7 i386 1.4.1-1 [330 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libgav1-1 i386 0.19.0-2+b1 [325 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 librav1e0 i386 0.7.1-2 [650 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libsharpyuv0 i386 1.3.2-0.4+b1 [107 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3 [169 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libyuv0 i386 0.0~git202401110.af6ac82-1 [108 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 libavif16 i386 1.0.4-2 [113 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libbsd0 i386 0.12.2-1 [134 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libde265-0 i386 1.0.15-1+b1 [195 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.2-1 [107 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libpng16-16t64 i386 1.6.43-5 [286 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 libfreetype6 i386 2.13.2+dfsg-1+b4 [449 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 libfontconfig1 i386 2.15.0-1.1 [401 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 libheif-plugin-dav1d i386 1.17.6-1+b2 [10.2 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 libheif-plugin-libde265 i386 1.17.6-1+b2 [13.7 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libheif1 i386 1.17.6-1+b2 [299 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libjbig0 i386 2.1-6.1+b1 [31.8 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 liblerc4 i386 4.0.0+ds-4+b1 [180 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libwebp7 i386 1.3.2-0.4+b1 [314 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libtiff6 i386 4.5.1+git230720-4 [338 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libxau6 i386 1:1.0.9-1+b1 [18.5 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libxdmcp6 i386 1:1.1.2-3+b1 [24.8 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libx11-data all 2:1.8.7-1 [328 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libx11-6 i386 2:1.8.7-1+b1 [822 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 libxpm4 i386 1:3.5.17-1+b1 [57.8 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libgd3 i386 2.3.3-9+b3 [129 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libg20 i386 0.72-12+b2 [42.6 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 libg2-dev i386 0.72-12+b2 [192 kB] Fetched 30.1 MB in 1s (60.0 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 ... 19683 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_i386.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_i386.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_i386.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_i386.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_i386.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../08-libpipeline1_1.5.7-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-2) ... 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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 i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config cp: warning: behavior of -n is non-portable and may change in future; use --update=none instead 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.m4:704: 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=i686-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/i386-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 -j22 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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -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 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 21 2.004905 0.318798 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 11 0.875129 0.498908 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 0.852581 1.100000 0.614043 1.200000 0.467741 1.300000 0.494580 1.400000 0.624001 1.500000 0.774492 1.600000 0.920132 1.700000 1.269933 1.800000 1.475483 1.900000 2.166812 2.000000 2.190547 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 -j22 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_i386.deb'. dpkg-deb: building package 'rnahybrid-dbgsym' in '../rnahybrid-dbgsym_2.1.2-8_i386.deb'. dpkg-genbuildinfo --build=binary -O../rnahybrid_2.1.2-8_i386.buildinfo dpkg-genchanges --build=binary -O../rnahybrid_2.1.2-8_i386.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/31867 and its subdirectories I: Current time: Tue Jun 10 02:46:38 -12 2025 I: pbuilder-time-stamp: 1749566798 Wed May 8 08:23:40 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Wed May 8 08:23:40 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Wed May 8 08:27:24 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Wed May 8 08:27:25 UTC 2024 I: rnahybrid_2.1.2-8_i386.changes: Format: 1.8 Date: Thu, 21 Dec 2023 19:49:33 +0100 Source: rnahybrid Binary: rnahybrid rnahybrid-dbgsym Architecture: i386 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: feab93798c7972f7a0cd707d92b7af19c18251a2 184004 rnahybrid-dbgsym_2.1.2-8_i386.deb 4ffb1ba95bfe3ed3eaf774aaa8cfd8b5ab5a1c61 6108 rnahybrid_2.1.2-8_i386.buildinfo 7adeb1aac6e992a2bfc88278ac6a6a827d8cf130 88872 rnahybrid_2.1.2-8_i386.deb Checksums-Sha256: 4011db38f0c94880b3f6bf0e01e79bfe7163db8622b891ea03d2c8a25d4b3361 184004 rnahybrid-dbgsym_2.1.2-8_i386.deb ce627ac392dc6cef15b0da20c17e87ed53a33cf4e46f681c9ebe4bc25b855334 6108 rnahybrid_2.1.2-8_i386.buildinfo d24432830d21d3fbac0321a3743df315fc3a09b557e97237c6a89d0e9efcc7c6 88872 rnahybrid_2.1.2-8_i386.deb Files: d8cdea6403a175199bbabb05660f08ae 184004 debug optional rnahybrid-dbgsym_2.1.2-8_i386.deb ff4f2d2dee65201832a51560daa485de 6108 science optional rnahybrid_2.1.2-8_i386.buildinfo d7d807de10f9c6513ae723dfd1d76a5e 88872 science optional rnahybrid_2.1.2-8_i386.deb Wed May 8 08:27:26 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_10-11021.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.A9yYrUPS/rnahybrid_2.1.2-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.A9yYrUPS/rnahybrid_2.1.2-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.A9yYrUPS/rnahybrid_2.1.2-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.A9yYrUPS/b1/rnahybrid_2.1.2-8_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.A9yYrUPS/b2/rnahybrid_2.1.2-8_i386.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: 0.489s) 0.489s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.022s) 0.022s 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: 909ms CPU time consumed: 908ms Wed May 8 08:27:28 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Wed May 8 08:27:28 UTC 2024 I: rnahybrid from trixie built successfully and reproducibly on i386. Wed May 8 08:27:29 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 8 08:27:29 UTC 2024 I: Submitting 8.0K b1/rnahybrid_2.1.2-8_i386.buildinfo.asc Wed May 8 08:27:30 UTC 2024 I: Submitting 8.0K b2/rnahybrid_2.1.2-8_i386.buildinfo.asc Wed May 8 08:27:32 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 8 08:27:32 UTC 2024 I: Done submitting .buildinfo files. Wed May 8 08:27:32 UTC 2024 I: Removing signed rnahybrid_2.1.2-8_i386.buildinfo.asc files: removed './b1/rnahybrid_2.1.2-8_i386.buildinfo.asc' removed './b2/rnahybrid_2.1.2-8_i386.buildinfo.asc'