I: pbuilder: network access will be disabled during build I: Current time: Fri Dec 6 14:13:17 +14 2024 I: pbuilder-time-stamp: 1733443997 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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_5.5.0-3.dsc] I: copying [./busco_5.5.0.orig.tar.gz] I: copying [./busco_5.5.0-3.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 5 18:33:36 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./busco_5.5.0-3.dsc: no acceptable signature found dpkg-source: info: extracting busco in busco-5.5.0 dpkg-source: info: unpacking busco_5.5.0.orig.tar.gz dpkg-source: info: unpacking busco_5.5.0-3.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 dpkg-source: info: applying python3.12-syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3524818/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Dec 6 00:13 /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/3524818/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3524818/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=6d7babc65c71492598e5f48c91e19def LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3524818 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.L2o0Wp2y/pbuilderrc_jC9h --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.L2o0Wp2y/b2 --logfile b2/build.log busco_5.5.0-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3524818/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, 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 ... 20086 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-sequence-python3; however: Package dh-sequence-python3 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} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{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} libcairo2{a} libcom-err2{a} libdebhelper-perl{a} libdeflate0{a} libdivsufsort3{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblcms2-2{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libopenjp2-7{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraqm0{a} libreadline8t64{a} libsharpyuv0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxrender1{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-all{a} python3-autocommand{a} python3-biopython{a} python3-cairo{a} python3-chardet{a} python3-dateutil{a} python3-freetype{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-rlpycairo{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-zipp{a} python3.12{a} python3.12-minimal{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} tzdata{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 fonts-dejavu-extra krb5-locales 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-numexpr python3-odf python3-olefile python3-openpyxl python3-scipy python3-tables shared-mime-info wget xdg-user-dirs 0 packages upgraded, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 73.9 MB of archives. After unpacking 315 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.12-minimal arm64 3.12.8-1 [808 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.12-minimal arm64 3.12.8-1 [1930 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2~rc1-2 [23.7 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 12 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libnsl2 arm64 1.3.0-3+b3 [37.9 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-5 [159 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libpython3.12-stdlib arm64 3.12.8-1 [1905 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 python3.12 arm64 3.12.8-1 [677 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.12.7-1 [9708 B] Get: 22 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.1-1 [850 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.1-1 [1988 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-6 [1130 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-11 [91.2 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-8 [517 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 47 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5+b1 [9239 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 75.2.0-1 [731 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20241024 [109 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libfontenc1 arm64 1:1.1.8-1+b1 [22.5 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+23.1 [216 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 xfonts-utils arm64 1:7.7+7 [89.3 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get: 77 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-1.1+b1 [318 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 hmmer arm64 3.4+dfsg-2+b1 [977 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.0-4 [98.7 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-1.1+b1 [387 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b2 [49.3 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b2 [27.2 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-9 [361 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1411 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.0.1-1 [441 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libimagequant0 arm64 2.18.0-1+b2 [34.6 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3+b1 [173 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.0-4 [1812 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 liblcms2-2 arm64 2.16-2 [151 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 libopenjp2-7 arm64 2.5.0-2+b4 [185 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.1-1 [1912 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libraqm0 arm64 0.10.1-1+b2 [13.8 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.4.0-0.1+b1 [112 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.4.0-0.1+b1 [268 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libwebpdemux2 arm64 1.4.0-0.1+b1 [110 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 libwebpmux3 arm64 1.4.0-0.1+b1 [122 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.1-1 [740 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 python3-all arm64 3.12.7-1 [1052 B] Get: 115 http://deb.debian.org/debian unstable/main arm64 python3-numpy arm64 1:1.26.4+ds-12 [3816 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 python3-pil arm64 10.4.0-1+b1 [498 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 python3-cairo arm64 1.26.1-2+b1 [130 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 python3-freetype all 2.5.1-1 [89.3 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 python3-rlpycairo all 0.3.0-3 [9904 B] Get: 121 http://deb.debian.org/debian unstable/main arm64 python3-reportlab all 4.2.5-1 [1117 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 xml-core all 0.19 [20.1 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 python3-biopython arm64 1.84+dfsg-4+b1 [1644 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 python3-tz all 2024.1-2 [30.9 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 python3-pandas-lib arm64 2.2.3+dfsg-5+b1 [6028 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Fetched 73.9 MB in 0s (210 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:arm64. (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 ... 20086 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-1_arm64.deb ... Unpacking libpython3.12-minimal:arm64 (3.12.8-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.6.4-1_arm64.deb ... Unpacking libexpat1:arm64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-1_arm64.deb ... Unpacking python3.12-minimal (3.12.8-1) ... Setting up libpython3.12-minimal:arm64 (3.12.8-1) ... Setting up libexpat1:arm64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-1) ... Selecting previously unselected package python3-minimal. (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 ... 20406 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_arm64.deb ... Unpacking python3-minimal (3.12.7-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:arm64. Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_arm64.deb ... Unpacking libcom-err2:arm64 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-3) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:arm64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_arm64.deb ... Unpacking libnsl2:arm64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../14-libreadline8t64_8.2-5_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:arm64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-1_arm64.deb ... Unpacking libpython3.12-stdlib:arm64 (3.12.8-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-1_arm64.deb ... Unpacking python3.12 (3.12.8-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... Selecting previously unselected package python3. (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 ... 21469 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_arm64.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../001-libpython3.13-minimal_3.13.1-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../002-python3.13-minimal_3.13.1-1_arm64.deb ... Unpacking python3.13-minimal (3.13.1-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../003-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../006-libmagic1t64_1%3a5.45-3+b1_arm64.deb ... 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Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../106-python3-pandas_2.2.3+dfsg-5_all.deb ... Unpacking python3-pandas (2.2.3+dfsg-5) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up libgraphite2-3:arm64 (1.3.14-2+b1) ... Setting up liblcms2-2:arm64 (2.16-2) ... Setting up libpixman-1-0:arm64 (0.44.0-3) ... Setting up libsharpyuv0:arm64 (1.4.0-0.1+b1) ... Setting up libxau6:arm64 (1:1.0.11-1) ... Setting up libxdmcp6:arm64 (1:1.1.5-1) ... Setting up libkeyutils1:arm64 (1.6.3-4) ... Setting up libxcb1:arm64 (1.17.0-2+b1) ... Setting up libicu72:arm64 (72.1-5+b1) ... Setting up liblerc4:arm64 (4.0.0+ds-5) ... Setting up bsdextrautils (2.40.2-11) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libxcb-render0:arm64 (1.17.0-2+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libbrotli1:arm64 (1.1.0-2+b6) ... Setting up libmagic1t64:arm64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libdeflate0:arm64 (1.22-1) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up libxcb-shm0:arm64 (1.17.0-2+b1) ... Setting up libcom-err2:arm64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:arm64 (2.1-6.1+b2) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up libkrb5support0:arm64 (1.21.3-3) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Dec 6 00:13:40 UTC 2024. Universal Time is now: Fri Dec 6 00:13:40 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libpython3.13-minimal:arm64 (3.13.1-1) ... Setting up libfontenc1:arm64 (1:1.1.8-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-0t64:arm64 (2.82.2-3) ... No schema files found: doing nothing. Setting up libblas3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libjpeg62-turbo:arm64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:arm64 (1.0.15-1) ... Setting up libimagequant0:arm64 (2.18.0-1+b2) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:arm64 (1.6.44-2) ... Setting up autopoint (0.22.5-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:arm64 (1.21.3-3) ... Setting up libgfortran5:arm64 (14.2.0-9) ... Setting up autoconf (2.72-3) ... Setting up libwebp7:arm64 (1.4.0-0.1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:arm64 (4.5.1+git230720-5) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up libopenjp2-7:arm64 (2.5.0-2+b4) ... Setting up python3.13-minimal (3.13.1-1) ... Setting up libx11-6:arm64 (2:1.8.10-2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:arm64 (1.21.3-3) ... Setting up libdivsufsort3:arm64 (2.0.1-6+b1) ... Setting up libwebpmux3:arm64 (1.4.0-0.1+b1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:arm64 (3.12.0-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libxrender1:arm64 (1:0.9.10-1.1+b2) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:arm64 (1.4.0-0.1+b1) ... Setting up libxext6:arm64 (2:1.3.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libfreetype6:arm64 (2.13.3+dfsg-1) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-3) ... Setting up libreadline8t64:arm64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up xml-core (0.19) ... Setting up hmmer (3.4+dfsg-2+b1) ... Setting up libharfbuzz0b:arm64 (10.0.1-1) ... Setting up libfontconfig1:arm64 (2.15.0-1.1+b1) ... Setting up libpython3.13-stdlib:arm64 (3.13.1-1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.1-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:arm64 (1.18.2-2) ... Setting up libraqm0:arm64 (0.10.1-1+b2) ... Setting up libnsl2:arm64 (1.3.0-3+b3) ... Setting up libpython3.12-stdlib:arm64 (3.12.8-1) ... Setting up python3.12 (3.12.8-1) ... Setting up debhelper (13.20) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libpython3-stdlib:arm64 (3.12.7-1) ... Setting up python3 (3.12.7-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-freetype (2.5.1-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-tz (2024.1-2) ... Setting up python3-pil:arm64 (10.4.0-1+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-cairo (1.26.1-2+b1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-all (3.12.7-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-reportlab (4.2.5-1) ... Setting up dh-python (6.20241024) ... Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.84+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 I: Building the package I: user script /srv/workspace/pbuilder/3524818/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3524818/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/busco-5.5.0/ && 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_5.5.0-3_source.changes dpkg-buildpackage: info: source package busco dpkg-buildpackage: info: source version 5.5.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it I: pybuild base:311: python3.12 setup.py clean 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.12' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py build I: pybuild base:311: /usr/bin/python3 setup.py build debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/busco-5.5.0' dh_auto_test -- --test-custom --test-args '{interpreter} -m unittest tests/unittest_runner.py -v' I: pybuild base:311: cd /build/reproducible-path/busco-5.5.0/.pybuild/cpython3_3.13/build; python3.13 -m unittest tests/unittest_runner.py -v /build/reproducible-path/busco-5.5.0/.pybuild/cpython3_3.13/build/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]" 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) ... 2024-12-06 14:15:26 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) ... 2024-12-06 14:15:26 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) ... 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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. 2024-12-06 14:15:26 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) ... 2024-12-06 14:15:26 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) ... 2024-12-06 14:15:26 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) ... 2024-12-06 14:15:26 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 0.794s OK (skipped=1) I: pybuild base:311: cd /build/reproducible-path/busco-5.5.0/.pybuild/cpython3_3.12/build; python3.12 -m unittest tests/unittest_runner.py -v /build/reproducible-path/busco-5.5.0/.pybuild/cpython3_3.12/build/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' "[^0-9][0-9]*:[0-9]*[^0-9]{0,1}[0-9]*[^0-9]{0,2}[0-9]*\[%s\]" 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) ... 2024-12-06 14:15:28 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) ... 2024-12-06 14:15:28 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) ... 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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. 2024-12-06 14:15:28 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) ... 2024-12-06 14:15:28 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) ... 2024-12-06 14:15:28 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) ... 2024-12-06 14:15:28 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 0.693s OK (skipped=1) make[1]: Leaving directory '/build/reproducible-path/busco-5.5.0' 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:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/busco-5.5.0/debian/busco /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3.13/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/busco-5.5.0/debian/busco /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3.12/dist-packages/busco/BuscoPlacer.py:211: SyntaxWarning: invalid escape sequence '\[' 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_5.5.0-3_arm64.deb'. dpkg-genbuildinfo --build=binary -O../busco_5.5.0-3_arm64.buildinfo dpkg-genchanges --build=binary -O../busco_5.5.0-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3524818/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3524818/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/3524818 and its subdirectories I: Current time: Fri Dec 6 14:15:35 +14 2024 I: pbuilder-time-stamp: 1733444135