I: pbuilder: network access will be disabled during build I: Current time: Fri Jul 16 02:57:51 +14 2021 I: pbuilder-time-stamp: 1626353871 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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_2.1.2-6.dsc] I: copying [./rnahybrid_2.1.2.orig.tar.gz] I: copying [./rnahybrid_2.1.2-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.pnDzvFhK/trustedkeys.kbx': General error gpgv: Signature made Thu Dec 3 07:01:29 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./rnahybrid_2.1.2-6.dsc 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_2.1.2-6.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4047/tmp/hooks/D01_modify_environment starting debug: Running on codethink12-arm64. 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 Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/4047/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4047/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=4047 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/tmp.UeuaQEm4I4/pbuilderrc_9NwK --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.UeuaQEm4I4/b2 --logfile b2/build.log --extrapackages usrmerge rnahybrid_2.1.2-6.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 16:26 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 04:38 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 04:38 more -rwsr-xr-x 1 root root 51360 Feb 8 04:38 mount -rwxr-xr-x 1 root root 14496 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 16 02:58 sh -> bash lrwxrwxrwx 1 root root 4 Jul 15 23:26 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 04:38 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 04:38 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/4047/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 ... 19646 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} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libg2-dev{a} libg20{a} libgd3{a} libicu67{a} libjbig0{a} libjpeg62-turbo{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libpipeline1{a} libpng16-16{a} libsigsegv2{a} libsub-override-perl{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} libxpm4{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} ucf{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, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 23.2 MB of archives. After unpacking 80.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 libwebp6 arm64 0.6.1-2.1 [244 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 libtiff5 arm64 4.2.0-1 [276 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.1-1 [310 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.1-1 [747 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libxpm4 arm64 1:3.5.12-1 [43.9 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libgd3 arm64 2.3.0-2 [127 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libg20 arm64 0.72-9+b1 [40.7 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libg2-dev arm64 0.72-9+b1 [190 kB] Fetched 23.2 MB in 0s (49.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package ucf. Preparing to unpack .../10-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../11-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-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 .../21-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... 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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 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (1238 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 22110 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... 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I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/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_2.1.2-6_source.changes dpkg-buildpackage: info: source package rnahybrid dpkg-buildpackage: info: source version 2.1.2-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille 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 aclocal: 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 thread-safe 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking g2.h usability... yes checking g2.h presence... yes checking for g2.h... yes checking g2_PS.h usability... yes checking g2_PS.h presence... 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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -c -o mt19937-1.o mt19937-1.c random.c: In function 'random_sequence': random.c:75:29: warning: implicit declaration of function 'calloc' [-Wimplicit-function-declaration] 75 | char *sequence = (char *) calloc(seqlen+1,sizeof(char)); | ^~~~~~ random.c:75:29: warning: incompatible implicit declaration of built-in function 'calloc' random.c:17:1: note: include '' or provide a declaration of 'calloc' 16 | #include +++ |+#include 17 | gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -c -o rnaeffective.o rnaeffective.c gcc -g -O2 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -fcommon -g -O2 -fdebug-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 15 2.026492 0.219870 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 15 -1.988441 1.365432 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 0.406211 1.100000 0.311127 1.200000 0.319629 1.300000 0.473805 1.400000 0.778265 1.500000 1.065619 1.600000 1.450201 1.700000 2.082143 1.800000 2.681296 1.900000 3.291073 2.000000 3.830707 Effective number: 1.100000 make[1]: Leaving directory '/build/rnahybrid-2.1.2' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install 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' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/rnahybrid-2.1.2/debian/rnahybrid/usr/bin' /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_2.1.2-6_arm64.deb'. dpkg-deb: building package 'rnahybrid-dbgsym' in '../rnahybrid-dbgsym_2.1.2-6_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../rnahybrid_2.1.2-6_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: user script /srv/workspace/pbuilder/4047/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4047/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/4047 and its subdirectories I: Current time: Fri Jul 16 03:11:08 +14 2021 I: pbuilder-time-stamp: 1626354668