I: pbuilder: network access will be disabled during build I: Current time: Sun May 26 01:41:35 +14 2024 I: pbuilder-time-stamp: 1716637295 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [busco_5.4.4-1.dsc] I: copying [./busco_5.4.4.orig.tar.gz] I: copying [./busco_5.4.4-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Jan 1 01:16:56 2023 +14 gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./busco_5.4.4-1.dsc: no acceptable signature found dpkg-source: info: extracting busco in busco-5.4.4 dpkg-source: info: unpacking busco_5.4.4.orig.tar.gz dpkg-source: info: unpacking busco_5.4.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-and-disable-tests.patch dpkg-source: info: applying find-bbmap-instead-of-bbtools.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3549301/tmp/hooks/D01_modify_environment starting debug: Running on ionos5-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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 26 01:41 /bin/sh -> /bin/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/3549301/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3549301/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(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=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=c4c4ffe89ea44d50b3f4bc916648367d 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=3549301 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/r-b-build.oepsScTz/pbuilderrc_3Blj --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oepsScTz/b2 --logfile b2/build.log --extrapackages usrmerge busco_5.4.4-1.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://85.184.249.68:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 2023 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 2023 more -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed lrwxrwxrwx 1 root root 9 May 26 01:41 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 2023 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/3549301/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 (= 13), dh-python, python3-all, python3-biopython, python3-pandas, python3-setuptools, hmmer dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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 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-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on hmmer; however: Package hmmer 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-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} hmmer{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} libreadline8{a} libsub-override-perl{a} libtiff6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxml2{a} m4{a} mailcap{a} man-db{a} media-types{a} mime-support{a} po-debconf{a} python3{a} python3-all{a} python3-biopython{a} python3-dateutil{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3-six{a} python3-tz{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} w3c-sgml-lib{a} x11-common{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-bottleneck python3-bs4 python3-html5lib python3-jinja2 python3-lxml python3-matplotlib python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-scipy python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 96 newly installed, 0 to remove and 0 not upgraded. Need to get 62.9 MB of archives. After unpacking 239 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get: 13 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-2 [131 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-4 [399 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1+b1 [189 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.1 [99.2 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.1 [109 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 82 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Fetched 62.9 MB in 1s (88.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. 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Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.70+nmu1_all.deb ... Unpacking mailcap (3.70+nmu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../5-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... 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Preparing to unpack .../52-libharfbuzz0b_6.0.0+dfsg-3_amd64.deb ... Unpacking libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Selecting previously unselected package libimagequant0:amd64. Preparing to unpack .../53-libimagequant0_2.17.0-1_amd64.deb ... Unpacking libimagequant0:amd64 (2.17.0-1) ... Selecting previously unselected package libjbig0:amd64. Preparing to unpack .../54-libjbig0_2.1-6.1_amd64.deb ... Unpacking libjbig0:amd64 (2.1-6.1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../55-libjpeg62-turbo_1%3a2.1.5-2_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-2) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../56-liblapack3_3.11.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../57-liblcms2-2_2.14-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.14-2) ... Selecting previously unselected package liblerc4:amd64. Preparing to unpack .../58-liblerc4_4.0.0+ds-2_amd64.deb ... Unpacking liblerc4:amd64 (4.0.0+ds-2) ... Selecting previously unselected package libopenjp2-7:amd64. Preparing to unpack .../59-libopenjp2-7_2.5.0-1+b1_amd64.deb ... Unpacking libopenjp2-7:amd64 (2.5.0-1+b1) ... Selecting previously unselected package libraqm0:amd64. Preparing to unpack .../60-libraqm0_0.7.0-4.1_amd64.deb ... Unpacking libraqm0:amd64 (0.7.0-4.1) ... Selecting previously unselected package libwebp7:amd64. Preparing to unpack .../61-libwebp7_1.2.4-0.1_amd64.deb ... Unpacking libwebp7:amd64 (1.2.4-0.1) ... Selecting previously unselected package libtiff6:amd64. Preparing to unpack .../62-libtiff6_4.5.0-5_amd64.deb ... Unpacking libtiff6:amd64 (4.5.0-5) ... Selecting previously unselected package libwebpdemux2:amd64. Preparing to unpack .../63-libwebpdemux2_1.2.4-0.1_amd64.deb ... Unpacking libwebpdemux2:amd64 (1.2.4-0.1) ... Selecting previously unselected package libwebpmux3:amd64. Preparing to unpack .../64-libwebpmux3_1.2.4-0.1_amd64.deb ... Unpacking libwebpmux3:amd64 (1.2.4-0.1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../65-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../66-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../67-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package python3-all. Preparing to unpack .../68-python3-all_3.11.2-1+b1_amd64.deb ... Unpacking python3-all (3.11.2-1+b1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../69-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-numpy. 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Not building database; man-db/auto-update is not 'true'. Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up python3-tz (2022.7.1-3) ... Setting up python3-six (1.16.0-4) ... Setting up python3-pil:amd64 (9.4.0-1.1+b1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-lib2to3 (3.11.2-2) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-2) ... Setting up dh-python (5.20230130) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... 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... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/3549301/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/3549301/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/busco-5.4.4/ && 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 > ../busco_5.4.4-1_source.changes dpkg-buildpackage: info: source package busco dpkg-buildpackage: info: source version 5.4.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3 --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:240: python3.11 setup.py clean 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --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:240: python3.11 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py build debian/rules override_dh_auto_test make[1]: Entering directory '/build/busco-5.4.4' dh_auto_test -- --test-custom --test-args '{interpreter} -m unittest tests/unittest_runner.py -v' I: pybuild base:240: cd /build/busco-5.4.4/.pybuild/cpython3_3.11/build; python3.11 -m unittest tests/unittest_runner.py -v test_cmdline_options_all_long (tests.unittests.run_BUSCO_unittests.TestParams.test_cmdline_options_all_long) ... ok test_cmdline_options_all_short (tests.unittests.run_BUSCO_unittests.TestParams.test_cmdline_options_all_short) ... ok test_cmdline_options_short_minimum (tests.unittests.run_BUSCO_unittests.TestParams.test_cmdline_options_short_minimum) ... ok test_command_line_cpu_type (tests.unittests.run_BUSCO_unittests.TestParams.test_command_line_cpu_type) ... ok test_command_line_evalue_type (tests.unittests.run_BUSCO_unittests.TestParams.test_command_line_evalue_type) ... ok test_command_line_limit_type (tests.unittests.run_BUSCO_unittests.TestParams.test_command_line_limit_type) ... ok test_help_long (tests.unittests.run_BUSCO_unittests.TestParams.test_help_long) ... ok test_help_short (tests.unittests.run_BUSCO_unittests.TestParams.test_help_short) ... ok test_version_long (tests.unittests.run_BUSCO_unittests.TestParams.test_version_long) ... ok test_version_short (tests.unittests.run_BUSCO_unittests.TestParams.test_version_short) ... ok test_config_main_configured (tests.unittests.ConfigManager_unittests.TestConfigManager.test_config_main_configured) ... ok test_config_main_validated (tests.unittests.ConfigManager_unittests.TestConfigManager.test_config_main_validated) ... ok test_get_config_from_env (tests.unittests.ConfigManager_unittests.TestConfigManager.test_get_config_from_env) ... ok test_get_config_from_params (tests.unittests.ConfigManager_unittests.TestConfigManager.test_get_config_from_params) ... ok test_autoconfig_init_adds_specific_parameters (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_adds_specific_parameters) ... ok test_autoconfig_init_calls_super (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_calls_super) ... ok test_autoconfig_init_creates_paths (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_creates_paths) ... ok test_autoconfig_init_downloads_lineage (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_downloads_lineage) ... ok test_autoconfig_init_loads_lineage_config (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_loads_lineage_config) ... ok test_autoconfig_init_propagates_mainconfig (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_propagates_mainconfig) ... 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_autoconfig_init_sets_results_dirname (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autoconfig_init_sets_results_dirname) ... ok test_autolineage_create_path_method_calls_parent (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_autolineage_create_path_method_calls_parent) ... 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_batch_mode_false_with_error (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_batch_mode_false_with_error) ... ok test_batch_mode_false_with_file (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_batch_mode_false_with_file) ... ok test_batch_mode_true (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_batch_mode_true) ... ok test_catch_disallowed_keys (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_catch_disallowed_keys) ... 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_check_lineage_present_false (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_false) ... 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_check_lineage_present_true_with_dataset_version_correct (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_true_with_dataset_version_correct) ... ok test_check_lineage_present_true_with_dataset_version_mismatch (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_true_with_dataset_version_mismatch) ... ok test_check_lineage_present_true_with_invalid_dataset_version (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_true_with_invalid_dataset_version) ... ok test_check_lineage_present_true_with_odb_missing (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_check_lineage_present_true_with_odb_missing) ... ok test_config_auto_lineage_both_selected_warning (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_auto_lineage_both_selected_warning) ... ok test_config_auto_lineage_dataset_specified_warning (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_auto_lineage_dataset_specified_warning) ... ok test_config_auto_lineage_none_selected_no_lineage_warning (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_auto_lineage_none_selected_no_lineage_warning) ... ok test_config_auto_lineage_settings (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_auto_lineage_settings) ... ok test_config_default_params (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_default_params) ... ok test_config_structure (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_structure) ... 2024-05-26 01:43:07 WARNING: Running Auto Lineage Selector as no lineage dataset was specified. This will take a little longer than normal. If you know what lineage dataset you want to use, please specify this in the config file or using the -l (--lineage-dataset) flag in the command line. ok test_config_update_args_bool (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_update_args_bool) ... 2024-05-26 01:43:07 INFO: Quiet mode selected. All subsequent INFO log messages to stdout suppressed. Detailed log still available in logs/busco.log ok test_config_update_args_nonbool (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_config_update_args_nonbool) ... ok test_create_required_paths (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_create_required_paths) ... ok test_downloader_initialized (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_downloader_initialized) ... ok test_evalue_default (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_evalue_default) ... ok test_evalue_nondefault (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_evalue_nondefault) ... ok test_expand_all_paths_hmmsearch (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_expand_all_paths_hmmsearch) ... ok test_expand_all_paths_relative_path_current_dir (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_expand_all_paths_relative_path_current_dir) ... ok test_expand_all_paths_relative_path_parent_dir (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_expand_all_paths_relative_path_parent_dir) ... ok test_expand_all_paths_tilde (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_expand_all_paths_tilde) ... ok test_limit_value_out_of_range (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_limit_value_out_of_range) ... ok test_limit_value_within_range (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_limit_value_within_range) ... ok test_log_config (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_log_config) ... ok test_mandatory_keys_check_log (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_mandatory_keys_check_log) ... ok test_mandatory_keys_check_missing_param_in (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_mandatory_keys_check_missing_param_in) ... ok test_mandatory_keys_check_missing_param_mode (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_mandatory_keys_check_missing_param_mode) ... ok test_mandatory_keys_check_missing_param_out (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_mandatory_keys_check_missing_param_out) ... ok test_out_value_check_invalid (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_out_value_check_invalid) ... ok test_out_value_check_valid (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_out_value_check_valid) ... ok test_previous_run_check_with_existing_run_and_restart (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_with_existing_run_and_restart) ... ok test_previous_run_check_with_existing_run_no_force (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_with_existing_run_no_force) ... ok test_previous_run_check_with_existing_run_with_force_and_log (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_with_existing_run_with_force_and_log) ... ok test_previous_run_check_without_existing_run (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_without_existing_run) ... ok test_previous_run_check_without_existing_run_and_restart (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_previous_run_check_without_existing_run_and_restart) ... ok test_propagate_config (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_propagate_config) ... ok test_read_config_file (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_read_config_file) ... ok test_read_config_file_duplicateerror (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_read_config_file_duplicateerror) ... ok test_read_config_file_ioerror (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_read_config_file_ioerror) ... ok test_read_config_file_parseerror (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_read_config_file_parseerror) ... ok test_required_input_exists_false (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_required_input_exists_false) ... ok test_set_results_dirname (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_set_results_dirname) ... ok test_validation (tests.unittests.BuscoConfig_unittests.TestBuscoConfig.test_validation) ... ok test_cleanup_disused_runs (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_cleanup_disused_runs) ... ok test_evaluate_first_order_tiebreak (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_first_order_tiebreak) ... ok test_evaluate_multiple_runners (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_multiple_runners) ... ok test_evaluate_second_order_tiebreak (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_second_order_tiebreak) ... ok test_evaluate_single_runner (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_single_runner) ... ok test_evaluate_third_order_tiebreak (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_evaluate_third_order_tiebreak) ... ok test_get_best_match_lineage (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_get_best_match_lineage) ... ok test_init_autolineage (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_init_autolineage) ... ok test_record_results_first_run (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_record_results_first_run) ... ok test_record_results_multiple_runs (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_record_results_multiple_runs) ... ok test_run_auto_selector_lineage_lists_no_virus (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_auto_selector_lineage_lists_no_virus) ... ok test_run_lineages_initializes_BuscoConfigAuto (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_lineages_initializes_BuscoConfigAuto) ... ok test_run_lineages_initializes_BuscoRunner (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_lineages_initializes_BuscoRunner) ... skipped 'Skipping for now, ends with Mock iterable error' test_run_lineages_returns_runners (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_lineages_returns_runners) ... ok test_run_lineages_runs_analysis (tests.unittests.AutoLineage_unittests.TestAutoLineage.test_run_lineages_runs_analysis) ... ok test_init_eukaryota_augustus_checks_filetype (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_init_eukaryota_augustus_checks_filetype) ... ok test_init_tools_eukaryota_augustus (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_init_tools_eukaryota_augustus) ... ok test_init_tools_eukaryota_metaeuk (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_init_tools_eukaryota_metaeuk) ... ok test_init_tools_prokaryota (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_init_tools_prokaryota) ... ok test_run_analysis_metaeuk (tests.unittests.GenomeAnalysis_unittests.TestConfigManager.test_run_analysis_metaeuk) ... ok test_auto_select_lineage_call_function_gets_lineage_dataset (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_gets_lineage_dataset) ... ok test_auto_select_lineage_call_function_initializes_asl (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_initializes_asl) ... ok test_auto_select_lineage_call_function_returns_lineage_dataset (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_returns_lineage_dataset) ... ok test_auto_select_lineage_call_function_returns_parent (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_returns_parent) ... ok test_auto_select_lineage_call_function_runs_asl (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_runs_asl) ... ok test_auto_select_lineage_call_function_selects_runner (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_auto_select_lineage_call_function_selects_runner) ... ok test_config_set_parent_dataset_if_not_virus (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_config_set_parent_dataset_if_not_virus) ... ok test_config_updated_if_lineage_missing (tests.unittests.BuscoRunner_unittests.TestAutoLineage.test_config_updated_if_lineage_missing) ... ok ---------------------------------------------------------------------- Ran 97 tests in 1.145s OK (skipped=1) make[1]: Leaving directory '/build/busco-5.4.4' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/busco/ -O--buildsystem=pybuild I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/busco-5.4.4/debian/busco /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild dh_installsystemduser -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_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -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 'busco' in '../busco_5.4.4-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../busco_5.4.4-1_amd64.buildinfo dpkg-genchanges --build=binary -O../busco_5.4.4-1_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: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3549301/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3549301/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/3549301 and its subdirectories I: Current time: Sun May 26 01:43:14 +14 2024 I: pbuilder-time-stamp: 1716637394