I: pbuilder: network access will be disabled during build I: Current time: Thu Feb 10 02:49:42 +14 2022 I: pbuilder-time-stamp: 1644410982 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 [barrnap_0.9+dfsg-2.dsc] I: copying [./barrnap_0.9+dfsg.orig.tar.xz] I: copying [./barrnap_0.9+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.hClJAh4Y/trustedkeys.kbx': General error gpgv: Signature made Sat Apr 18 00:04:01 2020 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./barrnap_0.9+dfsg-2.dsc dpkg-source: info: extracting barrnap in barrnap-0.9+dfsg dpkg-source: info: unpacking barrnap_0.9+dfsg.orig.tar.xz dpkg-source: info: unpacking barrnap_0.9+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_dirs dpkg-source: info: applying use_both_hmmsets I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3759499/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash 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/3759499/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3759499/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]="x86_64-pc-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=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=70533fa2ade848d9a35af06fc0a9dab1 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3759499 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.F3gs1yFOzm/pbuilderrc_Wgq3 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.F3gs1yFOzm/b2 --logfile b2/build.log barrnap_0.9+dfsg-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-11-amd64 #1 SMP Debian 5.10.92-1 (2022-01-18) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 5 2021 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 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 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jul 29 2021 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 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 29 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jul 29 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 29 2021 more -rwsr-xr-x 1 root root 55528 Jul 29 2021 mount -rwxr-xr-x 1 root root 18664 Jul 29 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Feb 10 02:49 sh -> bash lrwxrwxrwx 1 root root 4 Feb 7 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jul 29 2021 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 29 2021 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 29 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/3759499/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 12), hmmer (>= 3.1), lua5.1, bedtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 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 (= 12); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on hmmer (>= 3.1); however: Package hmmer is not installed. pbuilder-satisfydepends-dummy depends on lua5.1; however: Package lua5.1 is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools 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} bedtools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libdivsufsort3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} lua5.1{a} m4{a} man-db{a} po-debconf{a} readline-common{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, 37 newly installed, 0 to remove and 0 not upgraded. Need to get 20.5 MB of archives. After unpacking 78.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 bedtools amd64 2.30.0+dfsg-1 [663 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 lua5.1 amd64 5.1.5-8.1+b3 [99.9 kB] Fetched 20.5 MB in 0s (67.2 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 ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../05-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../06-libreadline8_8.1-1_amd64.deb ... Unpacking libreadline8:amd64 (8.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../09-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../12-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package bedtools. Preparing to unpack .../18-bedtools_2.30.0+dfsg-1_amd64.deb ... Unpacking bedtools (2.30.0+dfsg-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../19-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../20-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../21-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../22-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 .../23-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../24-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../25-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../26-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../27-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../28-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../29-libxml2_2.9.10+dfsg-6.7_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7) ... Selecting previously unselected package gettext. Preparing to unpack .../30-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../31-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../32-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../33-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libdivsufsort3:amd64. Preparing to unpack .../34-libdivsufsort3_2.0.1-5_amd64.deb ... Unpacking libdivsufsort3:amd64 (2.0.1-5) ... Selecting previously unselected package hmmer. Preparing to unpack .../35-hmmer_3.3.2+dfsg-1_amd64.deb ... Unpacking hmmer (3.3.2+dfsg-1) ... Selecting previously unselected package lua5.1. Preparing to unpack .../36-lua5.1_5.1.5-8.1+b3_amd64.deb ... Unpacking lua5.1 (5.1.5-8.1+b3) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up libelf1:amd64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up bedtools (2.30.0+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up m4 (1.4.18-5) ... Setting up lua5.1 (5.1.5-8.1+b3) ... update-alternatives: using /usr/bin/lua5.1 to provide /usr/bin/lua (lua-interpreter) in auto mode update-alternatives: using /usr/bin/luac5.1 to provide /usr/bin/luac (lua-compiler) in auto mode Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... 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... fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package hostname: Name or service not known I: Running cd /build/barrnap-0.9+dfsg/ && 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 > ../barrnap_0.9+dfsg-2_source.changes dpkg-buildpackage: info: source package barrnap dpkg-buildpackage: info: source version 0.9+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/barrnap-0.9+dfsg' rm -rf db/free make[1]: Leaving directory '/build/barrnap-0.9+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/barrnap-0.9+dfsg' # pass make[1]: Leaving directory '/build/barrnap-0.9+dfsg' dh_auto_test make -j15 test make[1]: Entering directory '/build/barrnap-0.9+dfsg' ./bin/barrnap examples/small.fna [barrnap] This is barrnap 0.9 [barrnap] Written by Torsten Seemann [barrnap] Obtained from https://github.com/tseemann/barrnap [barrnap] Detected operating system: linux [barrnap] Adding /build/barrnap-0.9+dfsg/bin/../binaries/linux to end of PATH [barrnap] Checking for dependencies: [barrnap] Found nhmmer - /usr/bin/nhmmer [barrnap] Found bedtools - /usr/bin/bedtools [barrnap] Will use 1 threads [barrnap] Setting evalue cutoff to 1e-06 [barrnap] Will tag genes < 0.8 of expected length. [barrnap] Will reject genes < 0.25 of expected length. [barrnap] Using database: /build/barrnap-0.9+dfsg/bin/../db/bac.hmm [barrnap] Scanning examples/small.fna for bac rRNA genes... please wait [barrnap] Command: nhmmer --cpu 1 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/build/barrnap-0.9+dfsg/bin/../db/bac.hmm' 'examples/small.fna' [barrnap] Found: 16S_rRNA P.marinus L=1480/1585 353314..354793 + 16S ribosomal RNA [barrnap] Found: 5S_rRNA P.marinus L=104/119 358433..358536 + 5S ribosomal RNA [barrnap] Found 2 ribosomal RNA features. [barrnap] Sorting features and outputting GFF3... [barrnap] Done. ##gff-version 3 P.marinus barrnap:0.9 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA P.marinus barrnap:0.9 rRNA 358433 358536 9.6e-07 + . Name=5S_rRNA;product=5S ribosomal RNA make[1]: Leaving directory '/build/barrnap-0.9+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/barrnap-0.9+dfsg' # pass make[1]: Leaving directory '/build/barrnap-0.9+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package barrnap: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'barrnap' in '../barrnap_0.9+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../barrnap_0.9+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3759499/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3759499/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/3759499 and its subdirectories I: Current time: Thu Feb 10 02:50:10 +14 2022 I: pbuilder-time-stamp: 1644411010