I: pbuilder: network access will be disabled during build I: Current time: Sun Jan 15 16:55:55 +14 2023 I: pbuilder-time-stamp: 1673751355 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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 [python-pymummer_0.10.3-2.dsc] I: copying [./python-pymummer_0.10.3.orig.tar.gz] I: copying [./python-pymummer_0.10.3-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Jan 7 22:42:14 2019 +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 ./python-pymummer_0.10.3-2.dsc dpkg-source: info: extracting python-pymummer in python-pymummer-0.10.3 dpkg-source: info: unpacking python-pymummer_0.10.3.orig.tar.gz dpkg-source: info: unpacking python-pymummer_0.10.3-2.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/171624/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash 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/171624/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/171624/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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(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 parallel=16' 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=ff35ccd6576f4df2a6faedc21ddd7539 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=171624 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.JP0ZTh9Gq2/pbuilderrc_NyyN --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.JP0ZTh9Gq2/b2 --logfile b2/build.log python-pymummer_0.10.3-2.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jan 15 16:56 sh -> bash lrwxrwxrwx 1 root root 4 Dec 11 18:20 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/171624/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 (>= 11~), dh-python, python3-all, python3-setuptools, fastaq (>= 3.10.0), mummer, python3-nose dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-all; however: Package python3-all is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on fastaq (>= 3.10.0); however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose 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} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} mummer{a} po-debconf{a} python3{a} python3-all{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-nose{a} python3-pkg-resources{a} python3-setuptools{a} python3.7{a} python3.7-minimal{a} readline-common{a} samtools{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl cwltool krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python shared-mime-info wget xdg-user-dirs 0 packages upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 30.6 MB of archives. After unpacking 113 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 gawk amd64 1:4.2.1+dfsg-1 [660 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 python3-distutils all 3.7.3-1 [142 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 dh-python all 3.20190308 [99.3 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 fastaq all 3.17.0-2 [47.8 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 mummer amd64 3.23+dfsg-4 [809 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 python3-all amd64 3.7.3-1 [1068 B] Get: 72 http://deb.debian.org/debian buster/main amd64 python3-nose all 1.3.7-4 [132 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 python3-setuptools all 40.8.0-1 [306 kB] Fetched 30.6 MB in 1s (41.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. 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Unpacking libsigsegv2:amd64 (2.12-2) ... Setting up readline-common (7.0-5) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package gawk. (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 ... 19862 files and directories currently installed.) Preparing to unpack .../gawk_1%3a4.2.1+dfsg-1_amd64.deb ... Unpacking gawk (1:4.2.1+dfsg-1) ... Selecting previously unselected package libssl1.1:amd64. 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Setting up libdeflate0:amd64 (1.2-1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up m4 (1.4.18-2) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libicu63:amd64 (63.1-6+deb10u1) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autotools-dev (20180224.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up autoconf (2.69-11) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up mummer (3.23+dfsg-4) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.4+dfsg1-7+deb10u2) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libtool (2.4.6-9) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libcroco3:amd64 (0.6.12-3) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3+deb10u1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up gettext (0.19.8.1-9) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up python3-setuptools (40.8.0-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up po-debconf (1.0.21) ... Setting up python3-all (3.7.3-1) ... Setting up python3-nose (1.3.7-4) ... Setting up samtools (1.9-4) ... Setting up fastaq (3.17.0-2) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 (1.23-1). 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/python-pymummer-0.10.3/ && 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 > ../python-pymummer_0.10.3-2_source.changes dpkg-buildpackage: info: source package python-pymummer dpkg-buildpackage: info: source version 0.10.3-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean LC_ALL=C.UTF-8 dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:217: python3.7 setup.py clean Checking MUMmer programs found in path: OK nucmer OK show-coords OK show-snps OK delta-filter running clean removing '/build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build' (and everything under it) 'build/bdist.linux-amd64' does not exist -- can't clean it 'build/scripts-3.7' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build LC_ALL=C.UTF-8 dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python3.7 setup.py config Checking MUMmer programs found in path: OK nucmer OK show-coords OK show-snps OK delta-filter running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py build Checking MUMmer programs found in path: OK nucmer OK show-coords OK show-snps OK delta-filter running build running build_py creating /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer copying pymummer/variant.py -> /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer copying pymummer/syscall.py -> /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer copying pymummer/snp_file.py -> /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer copying pymummer/snp.py -> /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer copying pymummer/nucmer.py -> /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer copying pymummer/coords_file.py -> /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer copying pymummer/alignment.py -> /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer copying pymummer/__init__.py -> /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer debian/rules override_dh_auto_test make[1]: Entering directory '/build/python-pymummer-0.10.3' PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="{interpreter} setup.py test" \ dh_auto_test I: pybuild base:217: python3.7 setup.py test Checking MUMmer programs found in path: OK nucmer OK show-coords OK show-snps OK delta-filter running test running egg_info creating pymummer.egg-info writing pymummer.egg-info/PKG-INFO writing dependency_links to pymummer.egg-info/dependency_links.txt writing requirements to pymummer.egg-info/requires.txt writing top-level names to pymummer.egg-info/top_level.txt writing manifest file 'pymummer.egg-info/SOURCES.txt' reading manifest file 'pymummer.egg-info/SOURCES.txt' writing manifest file 'pymummer.egg-info/SOURCES.txt' running build_ext test_init_nucmer (alignment_test.TestNucmer) test __init__ nucmer ... ok test_init_promer (alignment_test.TestNucmer) test __init__ promer ... ok test_intersects_variant (alignment_test.TestNucmer) Test intersects_variant ... ok test_is_self_hit (alignment_test.TestNucmer) Test is_self_hit ... ok test_on_same_strand (alignment_test.TestNucmer) test on_same_strand ... ok test_qry_coords (alignment_test.TestNucmer) Test qry_coords ... ok test_qry_coords_from_ref_coord_test_bad_ref_coord (alignment_test.TestNucmer) Test qry_coords_from_ref_coord with bad ref coords ... ok test_qry_coords_from_ref_coord_test_different_strand (alignment_test.TestNucmer) Test qry_coords_from_ref_coord on different strand ... ok test_qry_coords_from_ref_coord_test_same_strand (alignment_test.TestNucmer) Test qry_coords_from_ref_coord on same strand ... ok test_qry_coords_from_ref_coord_when_variant_not_in_nucmer_match (alignment_test.TestNucmer) Test ref_coords_from_qry_coord when variant not in nucmer match ... ok test_ref_coords (alignment_test.TestNucmer) Test ref_coords ... ok test_ref_coords_from_qry_coord_test_same_strand (alignment_test.TestNucmer) Test ref_coords_from_qry_coord on same strand ... ok test_ref_coords_from_qry_coord_when_variant_not_in_nucmer_match (alignment_test.TestNucmer) Test ref_coords_from_qry_coord when variant not in nucmer match ... ok test_reverse_query (alignment_test.TestNucmer) Test reverse_query ... ok test_reverse_reference (alignment_test.TestNucmer) Test reverse_reference ... ok test_str (alignment_test.TestNucmer) Test __str__ ... ok test_swap (alignment_test.TestNucmer) test swap ... ok test_to_msp_crunch (alignment_test.TestNucmer) Test to_msp_crunch ... ok test_convert_to_msp_crunch_no_offset (coords_file_test.TestCoordsFile) Test convert_to_msp_crunch with no offsets ... ok test_convert_to_msp_crunch_with_offset (coords_file_test.TestCoordsFile) Test convert_to_msp_crunch with offsets ... ok test_coords_file (coords_file_test.TestCoordsFile) test coords_file ... ok test_delta_filter_command (nucmer_test.TestRunner) test _delta_filter_command ... ok test_nucmer_command (nucmer_test.TestRunner) test _nucmer_command ... ok test_run_nucmer (nucmer_test.TestRunner) test run_nucmer ... ok test_show_coords_command (nucmer_test.TestRunner) test _show_coords_command ... ok test_show_snps_command (nucmer_test.TestRunner) test _show_snps_command ... ok test_write_script_no_snps (nucmer_test.TestRunner) test _write_script no snps ... ok test_write_script_with_snps (nucmer_test.TestRunner) test _write_script with snps ... ok test_get_all_variants (snp_file_test.TestUtils) Test load all variants from file ... ok test_snp_file (snp_file_test.TestUtils) test coords_file ... ok test_str_no_c_option (snp_test.TestSnp) Test __str__ with format with no -C option ... ok test_str_with_c_option (snp_test.TestSnp) Test __str__ with format with -C option ... ok test_run_fail (syscall_test.TestSyscall) Test that run raises error when command fails ... The following command failed with exit code 127 notacommandandthrowerror The output was: /bin/sh: notacommandandthrowerror: käsku ei ole ok test_run_ok (syscall_test.TestSyscall) Test run is ok on command that works ... ok test_init (variant_test.TestVariant) Test init gets correct variant type ... ok test_update_indel_deletion (variant_test.TestVariant) Test update_indel extends deletions correctly ... ok test_update_indel_insertion (variant_test.TestVariant) Test update_indel extends insertions correctly ... ok test_update_indel_no_change (variant_test.TestVariant) Test update_indel does nothing in the right cases ... ok ---------------------------------------------------------------------- Ran 38 tests in 0.724s OK make[1]: Leaving directory '/build/python-pymummer-0.10.3' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary LC_ALL=C.UTF-8 dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/python-pymummer-0.10.3/debian/python3-pymummer Checking MUMmer programs found in path: OK nucmer OK show-coords OK show-snps OK delta-filter running install running build running build_py running install_lib creating /build/python-pymummer-0.10.3/debian/python3-pymummer/usr creating /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib creating /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7 creating /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages creating /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer copying /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer/__init__.py -> /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer copying /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer/alignment.py -> /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer copying /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer/coords_file.py -> /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer copying /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer/nucmer.py -> /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer copying /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer/snp.py -> /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer copying /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer/snp_file.py -> /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer copying /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer/syscall.py -> /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer copying /build/python-pymummer-0.10.3/.pybuild/cpython3_3.7_pymummer/build/pymummer/variant.py -> /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer byte-compiling /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer/__init__.py to __init__.cpython-37.pyc byte-compiling /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer/alignment.py to alignment.cpython-37.pyc byte-compiling /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer/coords_file.py to coords_file.cpython-37.pyc byte-compiling /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer/nucmer.py to nucmer.cpython-37.pyc byte-compiling /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer/snp.py to snp.cpython-37.pyc byte-compiling /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer/snp_file.py to snp_file.cpython-37.pyc byte-compiling /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer/syscall.py to syscall.cpython-37.pyc byte-compiling /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer/variant.py to variant.cpython-37.pyc running install_egg_info running egg_info writing pymummer.egg-info/PKG-INFO writing dependency_links to pymummer.egg-info/dependency_links.txt writing requirements to pymummer.egg-info/requires.txt writing top-level names to pymummer.egg-info/top_level.txt reading manifest file 'pymummer.egg-info/SOURCES.txt' writing manifest file 'pymummer.egg-info/SOURCES.txt' Copying pymummer.egg-info to /build/python-pymummer-0.10.3/debian/python3-pymummer/usr/lib/python3.7/dist-packages/pymummer-0.10.3.egg-info Skipping SOURCES.txt running install_scripts dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installinit -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pymummer' in '../python3-pymummer_0.10.3-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../python-pymummer_0.10.3-2_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/171624/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/171624/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/171624 and its subdirectories I: Current time: Sun Jan 15 16:57:44 +14 2023 I: pbuilder-time-stamp: 1673751464