Mon May 22 07:03:40 UTC 2023 I: starting to build rnahybrid/bookworm/arm64 on jenkins on '2023-05-22 07:03' Mon May 22 07:03:40 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_27/28444/console.log Mon May 22 07:03:40 UTC 2023 I: Downloading source for bookworm/rnahybrid=2.1.2-7 --2023-05-22 07:03:40-- http://cdn-fastly.deb.debian.org/debian/pool/main/r/rnahybrid/rnahybrid_2.1.2-7.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2418 (2.4K) [text/prs.lines.tag] Saving to: ‘rnahybrid_2.1.2-7.dsc’ 0K .. 100% 13.5M=0s 2023-05-22 07:03:40 (13.5 MB/s) - ‘rnahybrid_2.1.2-7.dsc’ saved [2418/2418] Mon May 22 07:03:40 UTC 2023 I: rnahybrid_2.1.2-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: rnahybrid Binary: rnahybrid Architecture: any-amd64 any-i386 arm64 armhf mips mips64el mipsel ppc64el s390x alpha hppa m68k powerpc powerpcspe ppc64 sh4 sparc64 riscv64 Version: 2.1.2-7 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,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 011be163560b137447ef58588e05401c752e527d 7152 rnahybrid_2.1.2-7.debian.tar.xz Checksums-Sha256: e2bbbca714441f709732412a1a130e4911e212419af5b09154ddfaf0148d6e96 181984 rnahybrid_2.1.2.orig.tar.gz af53da27c47f37bfce9abd21bfbb77ee34d7d1ea0cb86f58acdea4a97e57d1ff 7152 rnahybrid_2.1.2-7.debian.tar.xz Files: 240f613f3fcc2f563f38804a54f07c89 181984 rnahybrid_2.1.2.orig.tar.gz 2813686ac1187030cf963364ae0536ad 7152 rnahybrid_2.1.2-7.debian.tar.xz Dgit: a22f87acc6a5bf9453b4112136559d4f05072d9a debian archive/debian/2.1.2-7 https://git.dgit.debian.org/rnahybrid -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmO5y0QUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqmsBAAgDKyfstoZC/2XRIZmQAz5XIhv0yN BN+R6SWCGrdwx7kTRYfQ3w/Wzz/OdnTPxfImLRQUFsr7Ger0rBbKsNRfXeEh8nWd dCQLtD/w8MHH6Ay3Rj0H8C4yJpUIm0eCvBLT45Zb0QPF8s9RMD2Mqje2c5jMPL03 HO5OMvqODXIg/aQwY39IBL+lGdHbaD7PYnqfURu5w+guarNAnxixzvZ6S1t+2ImK JyN9HBAAMZ3Cd2I9SmXhQJ0vbLXiMoH5u184PVq6j7jOA0ZaiRdgn1ubwVfnRP8L kdf2joljkBBmDkU1W62u7/NEjESJoEVod61cKlpNm0iIexcUzQytlPoWpY3e3X8Z 7DxQkao0S6IY/vmDdIcXT7fMK1uj67aT04mwXzpGxWJh2JeNdv3mbec0Q9gupMHH wPOz/y58UFTiw7i7RLuzddbYukBCbaGDmDVbf8X80UzyFxLwFTQy+ydZi2jyAAef ZvcqDgy6FjEqMmDXOBpuvoqWwIwpQhn0KNM1oMJuI0EPAhEy5g5pX5QGcfmgD1SN k1FK4D6e93yqii9D/TW02IRYWMHXF/8F1QAhz7b0c81p82/QQkCu9rcCXGAyGlUo apgxbqtyZEwReOBXsNFxHc0L/gkiyX4LDmIi0x5sbSRo+dTUnRJ0vPuzAiBnJrQ9 MhT78PMb3/pmPAo= =FMwP -----END PGP SIGNATURE----- Mon May 22 07:03:40 UTC 2023 I: Checking whether the package is not for us Mon May 22 07:03:40 UTC 2023 I: Starting 1st build on remote node codethink15-arm64.debian.net. Mon May 22 07:03:40 UTC 2023 I: Preparing to do remote build '1' on codethink15-arm64.debian.net. Mon May 22 07:25:12 UTC 2023 I: Deleting $TMPDIR on codethink15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 23 01:26:46 -12 2024 I: pbuilder-time-stamp: 1719149206 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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_2.1.2-7.dsc] I: copying [./rnahybrid_2.1.2.orig.tar.gz] I: copying [./rnahybrid_2.1.2-7.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 7 07:43:00 2023 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rnahybrid_2.1.2-7.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_2.1.2-7.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/11222/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='11222' 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.1Ha9t9j3/pbuilderrc_RnJU --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1Ha9t9j3/b1 --logfile b1/build.log rnahybrid_2.1.2-7.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink15-arm64 4.15.0-211-generic #222-Ubuntu SMP Tue Apr 18 18:58:27 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 20 04:47 /bin -> usr/bin I: user script /srv/workspace/pbuilder/11222/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: arm64 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 ... 19616 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} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libabsl20220623{a} libaom3{a} libarchive-zip-perl{a} libavif15{a} libbrotli1{a} libbsd0{a} libdav1d6{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libg2-dev{a} libg20{a} libgav1-1{a} libgd3{a} libheif1{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libnuma1{a} libpipeline1{a} libpng16-16{a} librav1e0{a} libsub-override-perl{a} libsvtav1enc1{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libx11-6{a} libx11-data{a} libx265-199{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 libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 29.0 MB of archives. After unpacking 110 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libabsl20220623 arm64 20220623.1-1 [363 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libaom3 arm64 3.6.0-1 [1379 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libdav1d6 arm64 1.0.0-2 [274 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libgav1-1 arm64 0.18.0-1+b1 [425 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 librav1e0 arm64 0.5.1-6 [552 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libsvtav1enc1 arm64 1.4.1+dfsg-1 [1074 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libyuv0 arm64 0.0~git20230123.b2528b0-1 [122 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libavif15 arm64 0.11.1-1 [88.3 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libde265-0 arm64 1.0.11-1 [148 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-5 [369 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libnuma1 arm64 2.0.16-1 [20.3 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libx265-199 arm64 3.5-2+b1 [603 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libheif1 arm64 1.15.1-1 [191 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.1 [259 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-5 [300 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libxpm4 arm64 1:3.5.12-1.1 [45.2 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libgd3 arm64 2.3.3-9 [113 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libg20 arm64 0.72-11 [38.1 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libg2-dev arm64 0.72-11 [188 kB] Fetched 29.0 MB in 1s (40.5 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 ... 19616 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... 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_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... 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 libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/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_2.1.2-7_source.changes dpkg-buildpackage: info: source package rnahybrid dpkg-buildpackage: info: source version 2.1.2-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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.m4:704: 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=aarch64-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/aarch64-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 -j8 make[1]: Entering directory '/build/rnahybrid-2.1.2' make all-recursive make[2]: Entering directory '/build/rnahybrid-2.1.2' Making all in src make[3]: Entering directory '/build/rnahybrid-2.1.2/src' gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -c -o rnaeffective.o rnaeffective.c gcc -g -O2 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 gcc -g -O2 -ffile-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -ffile-prefix-map=/build/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 make[3]: Leaving directory '/build/rnahybrid-2.1.2/src' Making all in man make[3]: Entering directory '/build/rnahybrid-2.1.2/man' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/rnahybrid-2.1.2/man' make[3]: Entering directory '/build/rnahybrid-2.1.2' make[3]: Leaving directory '/build/rnahybrid-2.1.2' make[2]: Leaving directory '/build/rnahybrid-2.1.2' make[1]: Leaving directory '/build/rnahybrid-2.1.2' debian/rules override_dh_auto_test make[1]: Entering directory '/build/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 1.860120 0.352850 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 21 0.029945 0.858304 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 1.037012 1.100000 0.754441 1.200000 0.558579 1.300000 0.439291 1.400000 0.450607 1.500000 0.534142 1.600000 0.665067 1.700000 0.846056 1.800000 1.126984 1.900000 1.399213 2.000000 1.666662 Effective number: 1.300000 make[1]: Leaving directory '/build/rnahybrid-2.1.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/rnahybrid/ make -j8 install DESTDIR=/build/rnahybrid-2.1.2/debian/rnahybrid AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/rnahybrid-2.1.2' Making install in src make[2]: Entering directory '/build/rnahybrid-2.1.2/src' make[3]: Entering directory '/build/rnahybrid-2.1.2/src' /usr/bin/mkdir -p '/build/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/install -c RNAhybrid RNAcalibrate RNAeffective '/build/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' make[3]: Leaving directory '/build/rnahybrid-2.1.2/src' make[2]: Leaving directory '/build/rnahybrid-2.1.2/src' Making install in man make[2]: Entering directory '/build/rnahybrid-2.1.2/man' make[3]: Entering directory '/build/rnahybrid-2.1.2/man' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/build/rnahybrid-2.1.2/debian/rnahybrid/usr/share/man/man1' /usr/bin/install -c -m 644 RNAhybrid.1 RNAcalibrate.1 RNAeffective.1 '/build/rnahybrid-2.1.2/debian/rnahybrid/usr/share/man/man1' make[3]: Leaving directory '/build/rnahybrid-2.1.2/man' make[2]: Leaving directory '/build/rnahybrid-2.1.2/man' make[2]: Entering directory '/build/rnahybrid-2.1.2' make[3]: Entering directory '/build/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/rnahybrid-2.1.2' make[2]: Leaving directory '/build/rnahybrid-2.1.2' make[1]: Leaving directory '/build/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_2.1.2-7_arm64.deb'. dpkg-deb: building package 'rnahybrid-dbgsym' in '../rnahybrid-dbgsym_2.1.2-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rnahybrid_2.1.2-7_arm64.buildinfo dpkg-genchanges --build=binary -O../rnahybrid_2.1.2-7_arm64.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/11222 and its subdirectories I: Current time: Sun Jun 23 01:48:11 -12 2024 I: pbuilder-time-stamp: 1719150491 Mon May 22 07:25:13 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink14-arm64.debian.net. Mon May 22 07:25:13 UTC 2023 I: Preparing to do remote build '2' on codethink14-arm64.debian.net. Mon May 22 07:47:28 UTC 2023 I: Deleting $TMPDIR on codethink14-arm64.debian.net. Mon May 22 07:47:29 UTC 2023 I: rnahybrid_2.1.2-7_arm64.changes: Format: 1.8 Date: Sat, 07 Jan 2023 18:32:46 +0100 Source: rnahybrid Binary: rnahybrid rnahybrid-dbgsym Architecture: arm64 Version: 2.1.2-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: rnahybrid - Fast and effective prediction of microRNA/target duplexes Closes: 1028122 Changes: rnahybrid (2.1.2-7) unstable; urgency=medium . * Team upload. . [ Eric Long ] * Add build target for riscv64 (Closes: #1028122) . [ Étienne Mollier ] * d/control: declare compliance to standards version 4.6.2. * fix-implicit-declaration.patch: add; fix implicit calloc declaration. * d/copyright: update copyright years. Checksums-Sha1: 2cb03d2cda997a3374eda0b15944dcb9e1e8bf3c 212768 rnahybrid-dbgsym_2.1.2-7_arm64.deb 75725e0a32e202082a729e0937e99e376e56e794 6068 rnahybrid_2.1.2-7_arm64.buildinfo b0f3bd51973f1a20efdccba33fd29ad916879cc9 82288 rnahybrid_2.1.2-7_arm64.deb Checksums-Sha256: 12f9776073a01cc6052fd6f9e3c6fa8675c4f2ee27597b28be5779df01032c19 212768 rnahybrid-dbgsym_2.1.2-7_arm64.deb 16a84cf3d7287a64feab9fc465c87ce635baefb7c5dc8077a90075d1ecb33672 6068 rnahybrid_2.1.2-7_arm64.buildinfo b8b10a59cba35e8fd77ae64cfce5254d9e817e0ba6b8f1df2f365836465f228d 82288 rnahybrid_2.1.2-7_arm64.deb Files: 7d55f24d1004dc9a609da4744f1cacf1 212768 debug optional rnahybrid-dbgsym_2.1.2-7_arm64.deb a25c2ecbdd115927139520b8117aca4f 6068 science optional rnahybrid_2.1.2-7_arm64.buildinfo b5ab759adc96ab90dd2606e8836d2940 82288 science optional rnahybrid_2.1.2-7_arm64.deb Mon May 22 07:47:30 UTC 2023 I: diffoscope 242 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.1Ha9t9j3/rnahybrid_2.1.2-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.1Ha9t9j3/rnahybrid_2.1.2-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.1Ha9t9j3/rnahybrid_2.1.2-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.1Ha9t9j3/b1/rnahybrid_2.1.2-7_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.1Ha9t9j3/b2/rnahybrid_2.1.2-7_arm64.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: 0.393s) 0.393s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.026s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon May 22 07:47:33 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists. Mon May 22 07:47:33 UTC 2023 I: rnahybrid from bookworm built successfully and reproducibly on arm64. Mon May 22 07:47:34 UTC 2023 I: Submitting .buildinfo files to external archives: Mon May 22 07:47:34 UTC 2023 I: Submitting 8.0K b1/rnahybrid_2.1.2-7_arm64.buildinfo.asc Mon May 22 07:47:35 UTC 2023 I: Submitting 8.0K b2/rnahybrid_2.1.2-7_arm64.buildinfo.asc Mon May 22 07:47:36 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon May 22 07:47:36 UTC 2023 I: Done submitting .buildinfo files. Mon May 22 07:47:36 UTC 2023 I: Removing signed rnahybrid_2.1.2-7_arm64.buildinfo.asc files: removed './b1/rnahybrid_2.1.2-7_arm64.buildinfo.asc' removed './b2/rnahybrid_2.1.2-7_arm64.buildinfo.asc'