I: pbuilder: network access will be disabled during build I: Current time: Thu May 18 09:09:36 +14 2023 I: pbuilder-time-stamp: 1684350576 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 [mirtop_0.4.25-2.dsc] I: copying [./mirtop_0.4.25.orig.tar.gz] I: copying [./mirtop_0.4.25-2.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Dec 3 11:36:25 2022 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./mirtop_0.4.25-2.dsc: no acceptable signature found dpkg-source: info: extracting mirtop in mirtop-0.4.25 dpkg-source: info: unpacking mirtop_0.4.25.orig.tar.gz dpkg-source: info: unpacking mirtop_0.4.25-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying fix-circular-import.patch dpkg-source: info: applying pytest.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4161939/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 18 09:09 /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/4161939/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/4161939/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=15 ' 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=57799774ad3b42e4a22181762e5bccad 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=4161939 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.K9YE8GrD/pbuilderrc_M50s --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.K9YE8GrD/b2 --logfile b2/build.log --extrapackages usrmerge mirtop_0.4.25-2.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 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 03:20 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 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 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 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 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 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 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 09:55 sed lrwxrwxrwx 1 root root 9 May 18 09:09 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 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 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 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 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 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 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/4161939/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-setuptools, python3-sphinx, python3-recommonmark, python3-pysam, python3-pybedtools, python3-pandas, python3-biopython 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-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on python3-recommonmark; however: Package python3-recommonmark is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-pybedtools; however: Package python3-pybedtools is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython 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} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-urw-base35{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{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} libhts3{a} libhtscodecs2{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenjp2-7{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{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} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-all{a} python3-babel{a} python3-biopython{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-commonmark{a} python3-dateutil{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-numpy{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pkg-resources{a} python3-pybedtools{a} python3-pygments{a} python3-pysam{a} python3-recommonmark{a} python3-renderpm{a} python3-reportlab{a} python3-reportlab-accel{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-tz{a} python3-urllib3{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{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: curl javascript-common libarchive-cpio-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libpaper-utils libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-bottleneck python3-bs4 python3-html5lib 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, 134 newly installed, 0 to remove and 0 not upgraded. Need to get 88.4 MB of archives. After unpacking 311 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 openssl amd64 3.0.8-1 [1407 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-1+b1 [189 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.1 [285 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-5 [316 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.1 [99.2 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.1 [109 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 python-babel-localedata all 2.10.3-1 [5615 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 python3-alabaster all 0.7.12-1 [20.8 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get: 100 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-3 [30.1 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 python3-babel all 2.10.3-1 [103 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 python3-commonmark all 0.9.1-4 [45.1 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 116 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get: 117 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get: 118 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get: 119 http://deb.debian.org/debian bookworm/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 120 http://deb.debian.org/debian bookworm/main amd64 python3-markupsafe amd64 2.1.2-1+b1 [13.2 kB] Get: 121 http://deb.debian.org/debian bookworm/main amd64 python3-jinja2 all 3.1.2-1 [119 kB] Get: 122 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get: 123 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get: 124 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get: 125 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get: 126 http://deb.debian.org/debian bookworm/main amd64 python3-pybedtools amd64 0.9.0-4+b1 [12.2 MB] Get: 127 http://deb.debian.org/debian bookworm/main amd64 python3-pygments all 2.14.0+dfsg-1 [783 kB] Get: 128 http://deb.debian.org/debian bookworm/main amd64 sphinx-common all 5.3.0-4 [653 kB] Get: 129 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get: 130 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get: 131 http://deb.debian.org/debian bookworm/main amd64 python3-snowballstemmer all 2.2.0-2 [57.8 kB] Get: 132 http://deb.debian.org/debian bookworm/main amd64 python3-sphinx all 5.3.0-4 [549 kB] Get: 133 http://deb.debian.org/debian bookworm/main amd64 python3-recommonmark all 0.7.1+ds-5 [17.3 kB] Get: 134 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Fetched 88.4 MB in 9s (9679 kB/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. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 19912 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_amd64.deb ... 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 ... (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 ... 20370 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.31_all.deb ... Unpacking sgml-base (1.31) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../003-openssl_3.0.8-1_amd64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../004-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../006-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../009-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../012-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../014-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../015-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../016-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../017-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../018-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../019-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../020-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../021-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../022-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../023-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../024-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../025-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../026-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../027-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../028-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../029-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../030-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../031-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../032-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../033-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../034-python3-lib2to3_3.11.2-3_all.deb ... Unpacking python3-lib2to3 (3.11.2-3) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../035-python3-distutils_3.11.2-3_all.deb ... Unpacking python3-distutils (3.11.2-3) ... Selecting previously unselected package dh-python. Preparing to unpack .../036-dh-python_5.20230130_all.deb ... Unpacking dh-python (5.20230130) ... Selecting previously unselected package xml-core. Preparing to unpack .../037-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package docutils-common. Preparing to unpack .../038-docutils-common_0.19+dfsg-6_all.deb ... Unpacking docutils-common (0.19+dfsg-6) ... Selecting previously unselected package libfontenc1:amd64. Preparing to unpack .../039-libfontenc1_1%3a1.1.4-1_amd64.deb ... Unpacking libfontenc1:amd64 (1:1.1.4-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../040-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../041-libpng16-16_1.6.39-2_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../042-libfreetype6_2.12.1+dfsg-5_amd64.deb ... Unpacking libfreetype6:amd64 (2.12.1+dfsg-5) ... Selecting previously unselected package x11-common. Preparing to unpack .../043-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package xfonts-encodings. Preparing to unpack .../044-xfonts-encodings_1%3a1.0.4-2.2_all.deb ... Unpacking xfonts-encodings (1:1.0.4-2.2) ... Selecting previously unselected package xfonts-utils. Preparing to unpack .../045-xfonts-utils_1%3a7.7+6_amd64.deb ... Unpacking xfonts-utils (1:7.7+6) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../046-fonts-urw-base35_20200910-7_all.deb ... Unpacking fonts-urw-base35 (20200910-7) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../047-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../048-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../049-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../050-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../051-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... 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Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up python-babel-localedata (2.10.3-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.2.4-0.1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:amd64 (4.5.0-5) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libjson-perl (4.10000-1) ... Setting up libopenjp2-7:amd64 (2.5.0-1+b1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.0.8-1) ... Setting up libwebpmux3:amd64 (1.2.4-0.1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up mailcap (3.70+nmu1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 (1.13.1-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.7-5) ... Setting up libwebpdemux2:amd64 (1.2.4-0.1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up xml-core (0.18+nmu1) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up sphinx-common (5.3.0-4) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up python3-markupsafe (2.1.2-1+b1) ... 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-roman (3.3-3) ... Setting up python3-jinja2 (3.1.2-1) ... Setting up python3-packaging (23.0-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-snowballstemmer (2.2.0-2) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-idna (3.3-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-commonmark (0.9.1-4) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-babel (2.10.3-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-alabaster (0.7.12-1) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-pygments (2.14.0+dfsg-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-pybedtools (0.9.0-4+b1) ... 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 docutils-common (0.19+dfsg-6) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-sphinx (5.3.0-4) ... Setting up python3-recommonmark (0.7.1+ds-5) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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/4161939/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/4161939/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/mirtop-0.4.25/ && 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 > ../mirtop_0.4.25-2_source.changes dpkg-buildpackage: info: source package mirtop dpkg-buildpackage: info: source version 0.4.25-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from mirtop-0.4.25/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p 3.11 I: pybuild base:240: python3.11 setup.py clean running clean removing '/build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.11' does not exist -- can't clean it rm -rf .pybuild/ find . -name \*.pyc -exec rm {} \; dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/python3-mirtop.substvars debian/mirtop.substvars ./mirtop/version.py debian/files rm -fr -- debian/python3-mirtop/ debian/tmp/ debian/mirtop/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.11 I: pybuild base:240: python3.11 setup.py config running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/mirtop-0.4.25' dh_auto_build pybuild --build -i python{version} -p 3.11 I: pybuild base:240: /usr/bin/python3 setup.py build running build running build_py creating /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop copying mirtop/version.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop copying mirtop/__init__.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop copying mirtop/install.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop copying mirtop/command_line.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop creating /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/sql copying mirtop/sql/sql.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/sql copying mirtop/sql/__init__.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/sql creating /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer copying mirtop/importer/srnabench.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer copying mirtop/importer/isomirsea.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer copying mirtop/importer/__init__.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer copying mirtop/importer/manatee.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer copying mirtop/importer/prost.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer copying mirtop/importer/optimir.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer copying mirtop/importer/seqbuster.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer creating /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter copying mirtop/exporter/__init__.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter copying mirtop/exporter/fasta.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter copying mirtop/exporter/isomirs.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter copying mirtop/exporter/seqbuster.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter copying mirtop/exporter/vcf.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter creating /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/validator.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/query.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/compare.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/update.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/__init__.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/convert.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/stats.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/gff_versions.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/classgff.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/check.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/header.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/read.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/body.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff copying mirtop/gff/merge.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff creating /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/bam copying mirtop/bam/bam.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/bam copying mirtop/bam/__init__.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/bam copying mirtop/bam/filter.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/bam creating /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/fastq.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/do.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/logger.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/utils.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/sql.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/__init__.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/parse.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/read.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/config.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/simulator.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs copying mirtop/libs/spikeins.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs creating /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna copying mirtop/mirna/__init__.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna copying mirtop/mirna/annotate.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna copying mirtop/mirna/mintplates.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna copying mirtop/mirna/fasta.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna copying mirtop/mirna/snps.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna copying mirtop/mirna/keys.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna copying mirtop/mirna/realign.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna copying mirtop/mirna/mapper.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna running egg_info creating mirtop.egg-info writing mirtop.egg-info/PKG-INFO writing dependency_links to mirtop.egg-info/dependency_links.txt writing entry points to mirtop.egg-info/entry_points.txt writing top-level names to mirtop.egg-info/top_level.txt writing manifest file 'mirtop.egg-info/SOURCES.txt' reading manifest file 'mirtop.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'mirtop.egg-info/SOURCES.txt' PYTHONPATH=. python3 -m sphinx -N -bman docs/ build/man # Manpage generator Running Sphinx v5.3.0 WARNING: Invalid configuration value found: 'language = None'. Update your configuration to a valid language code. Falling back to 'en' (English). making output directory... done WARNING: html_static_path entry '_static' does not exist building [mo]: targets for 0 po files that are out of date building [man]: all manpages updating environment: [new config] 11 added, 0 changed, 0 removed reading sources... [ 9%] CONTRIBUTING reading sources... [ 18%] code /usr/lib/python3/dist-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module. warnings.warn( /build/mirtop-0.4.25/mirtop/mirna/mintplates.py:512: SyntaxWarning: "is" with a literal. Did you mean "=="? if prefix is '': reading sources... [ 27%] code_structure reading sources... [ 36%] competition reading sources... [ 45%] how_to_contribute reading sources... [ 54%] index reading sources... [ 63%] installation reading sources... [ 72%] issue_template reading sources... [ 81%] output reading sources... [ 90%] quick_start reading sources... [100%] sql_usage /build/mirtop-0.4.25/mirtop/gff/body.py:docstring of mirtop.gff.body.lift_to_genome:7: ERROR: Unexpected indentation. /build/mirtop-0.4.25/mirtop/mirna/realign.py:docstring of mirtop.mirna.realign.hits:1: WARNING: duplicate object description of mirtop.mirna.realign.hits, other instance in code, use :noindex: for one of them /build/mirtop-0.4.25/mirtop/mirna/realign.py:docstring of mirtop.mirna.realign.isomir:1: WARNING: duplicate object description of mirtop.mirna.realign.isomir, other instance in code, use :noindex: for one of them /build/mirtop-0.4.25/mirtop/mirna/realign.py:docstring of mirtop.mirna.realign.isomir.format:1: WARNING: duplicate object description of mirtop.mirna.realign.isomir.format, other instance in code, use :noindex: for one of them /build/mirtop-0.4.25/mirtop/mirna/realign.py:docstring of mirtop.mirna.realign.isomir.formatGFF:1: WARNING: duplicate object description of mirtop.mirna.realign.isomir.formatGFF, other instance in code, use :noindex: for one of them /build/mirtop-0.4.25/mirtop/mirna/realign.py:docstring of mirtop.mirna.realign.isomir.format_id:1: WARNING: duplicate object description of mirtop.mirna.realign.isomir.format_id, other instance in code, use :noindex: for one of them /build/mirtop-0.4.25/mirtop/mirna/realign.py:docstring of mirtop.mirna.realign.isomir.get_score:1: WARNING: duplicate object description of mirtop.mirna.realign.isomir.get_score, other instance in code, use :noindex: for one of them /build/mirtop-0.4.25/mirtop/mirna/realign.py:docstring of mirtop.mirna.realign.isomir.is_iso:1: WARNING: duplicate object description of mirtop.mirna.realign.isomir.is_iso, other instance in code, use :noindex: for one of them /build/mirtop-0.4.25/mirtop/mirna/realign.py:docstring of mirtop.mirna.realign.isomir.set_pos:1: WARNING: duplicate object description of mirtop.mirna.realign.isomir.set_pos, other instance in code, use :noindex: for one of them /build/mirtop-0.4.25/docs/code_structure.md:5: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/code_structure.md:6: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/code_structure.md:12: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/code_structure.md:13: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/code_structure.md:24: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/code_structure.md:25: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/code_structure.md:39: WARNING: Bullet list ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/how_to_contribute.md:10: WARNING: Bullet list ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/how_to_contribute.md:15: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:30: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/how_to_contribute.md:31: WARNING: Definition list ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/how_to_contribute.md:31: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:31: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:38: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/how_to_contribute.md:36: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:42: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/how_to_contribute.md:42: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:42: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:54: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:54: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:56: WARNING: Definition list ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/how_to_contribute.md:56: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:56: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:62: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:62: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:64: WARNING: Definition list ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/how_to_contribute.md:64: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:64: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:90: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:90: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:89: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/how_to_contribute.md:92: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:92: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:109: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:109: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:101: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/how_to_contribute.md:104: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/how_to_contribute.md:107: WARNING: Definition list ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/how_to_contribute.md:111: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/how_to_contribute.md:111: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/installation.md:21: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/installation.md:35: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/installation.md:35: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:14: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/sql_usage.md:7: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:26: WARNING: Option list ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/sql_usage.md:35: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/sql_usage.md:36: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/sql_usage.md:51: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/sql_usage.md:58: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/sql_usage.md:62: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:115: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/sql_usage.md:113: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:121: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/sql_usage.md:121: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:121: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:135: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/sql_usage.md:132: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:148: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/sql_usage.md:148: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:148: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:156: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:195: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:195: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:201: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:219: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:219: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:229: ERROR: Unexpected indentation. /build/mirtop-0.4.25/docs/sql_usage.md:227: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:230: WARNING: Block quote ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/sql_usage.md:234: WARNING: Definition list ends without a blank line; unexpected unindent. /build/mirtop-0.4.25/docs/sql_usage.md:234: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:238: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:245: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:245: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:358: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:364: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:364: WARNING: Inline interpreted text or phrase reference start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:387: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:397: WARNING: Inline literal start-string without end-string. /build/mirtop-0.4.25/docs/sql_usage.md:397: WARNING: Inline interpreted text or phrase reference start-string without end-string. looking for now-outdated files... none found pickling environment... done checking consistency... /build/mirtop-0.4.25/docs/CONTRIBUTING.md: WARNING: document isn't included in any toctree /build/mirtop-0.4.25/docs/issue_template.md: WARNING: document isn't included in any toctree /build/mirtop-0.4.25/docs/sql_usage.md: WARNING: document isn't included in any toctree done writing... mirtop.1 { competition installation quick_start output code_structure how_to_contribute code } done build succeeded, 95 warnings. The manual pages are in build/man. make[1]: Leaving directory '/build/mirtop-0.4.25' rm -f debian/mirtop.debhelper.log debian/python3-mirtop.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/mirtop-0.4.25' # No tests, yet Not testing. make[1]: Leaving directory '/build/mirtop-0.4.25' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/python3-mirtop.substvars debian/mirtop.substvars rm -fr -- debian/.debhelper/generated/python3-mirtop/ debian/python3-mirtop/ debian/tmp/ debian/.debhelper/generated/mirtop/ debian/mirtop/ dh_auto_install -O--buildsystem=pybuild install -m0755 -d /build/mirtop-0.4.25/debian/tmp pybuild --install -i python{version} -p 3.11 --dest-dir /build/mirtop-0.4.25/debian/tmp I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/mirtop-0.4.25/debian/python3-mirtop running install /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( running build running build_py copying mirtop/version.py -> /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop running egg_info writing mirtop.egg-info/PKG-INFO writing dependency_links to mirtop.egg-info/dependency_links.txt writing entry points to mirtop.egg-info/entry_points.txt writing top-level names to mirtop.egg-info/top_level.txt reading manifest file 'mirtop.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'mirtop.egg-info/SOURCES.txt' running install_lib creating /build/mirtop-0.4.25/debian/python3-mirtop creating /build/mirtop-0.4.25/debian/python3-mirtop/usr creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11 creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/version.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna/mapper.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna/realign.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna/keys.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna/snps.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna/fasta.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna/mintplates.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna/annotate.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/mirna/__init__.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/spikeins.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/simulator.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/config.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/read.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/parse.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/__init__.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/sql.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/utils.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/logger.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/do.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/libs/fastq.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/bam copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/bam/filter.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/bam copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/bam/__init__.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/bam copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/bam/bam.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/bam creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/merge.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/body.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/read.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/header.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/check.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/classgff.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/gff_versions.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/stats.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/convert.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/__init__.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/update.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/compare.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/query.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/gff/validator.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter/vcf.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter/seqbuster.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter/isomirs.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter/fasta.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/exporter/__init__.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer/seqbuster.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer/optimir.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer/prost.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer/manatee.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer/__init__.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer/isomirsea.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/importer/srnabench.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer creating /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/sql copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/sql/__init__.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/sql copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/sql/sql.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/sql copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/command_line.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/install.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop copying /build/mirtop-0.4.25/.pybuild/cpython3_3.11_mirtop/build/mirtop/__init__.py -> /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/version.py to version.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna/mapper.py to mapper.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna/realign.py to realign.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna/keys.py to keys.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna/snps.py to snps.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna/fasta.py to fasta.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna/mintplates.py to mintplates.cpython-311.pyc /usr/lib/python3.11/dist-packages/mirtop/mirna/mintplates.py:512: SyntaxWarning: "is" with a literal. Did you mean "=="? byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna/annotate.py to annotate.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/mirna/__init__.py to __init__.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/spikeins.py to spikeins.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/simulator.py to simulator.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/config.py to config.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/read.py to read.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/parse.py to parse.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/__init__.py to __init__.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/sql.py to sql.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/utils.py to utils.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/logger.py to logger.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/do.py to do.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/libs/fastq.py to fastq.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/bam/filter.py to filter.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/bam/__init__.py to __init__.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/bam/bam.py to bam.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/merge.py to merge.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/body.py to body.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/read.py to read.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/header.py to header.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/check.py to check.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/classgff.py to classgff.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/gff_versions.py to gff_versions.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/stats.py to stats.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/convert.py to convert.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/__init__.py to __init__.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/update.py to update.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/compare.py to compare.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/query.py to query.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/gff/validator.py to validator.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter/vcf.py to vcf.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter/seqbuster.py to seqbuster.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter/isomirs.py to isomirs.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter/fasta.py to fasta.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/exporter/__init__.py to __init__.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer/seqbuster.py to seqbuster.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer/optimir.py to optimir.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer/prost.py to prost.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer/manatee.py to manatee.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer/__init__.py to __init__.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer/isomirsea.py to isomirsea.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/importer/srnabench.py to srnabench.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/sql/__init__.py to __init__.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/sql/sql.py to sql.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/command_line.py to command_line.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/install.py to install.cpython-311.pyc byte-compiling /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop/__init__.py to __init__.cpython-311.pyc running install_egg_info Copying mirtop.egg-info to /build/mirtop-0.4.25/debian/python3-mirtop/usr/lib/python3.11/dist-packages/mirtop-0.4.25.egg-info Skipping SOURCES.txt running install_scripts Installing mirtop script to /build/mirtop-0.4.25/debian/python3-mirtop/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/mirtop-0.4.25' dh_install install -m0755 -d debian/mirtop/usr/bin cp --reflink=auto -a ./debian/python3-mirtop/usr/bin/mirtop debian/mirtop/usr/bin/ rm debian/python3-mirtop/usr/bin/mirtop make[1]: Leaving directory '/build/mirtop-0.4.25' dh_installdocs -O--buildsystem=pybuild install -m0755 -d debian/python3-mirtop/usr/share/doc/python3-mirtop install -m0755 -d debian/python3-mirtop/usr/share/doc/python3-mirtop cp --reflink=auto -a ./README.md debian/python3-mirtop/usr/share/doc/python3-mirtop cp --reflink=auto -a ./debian/README.test debian/python3-mirtop/usr/share/doc/python3-mirtop cp --reflink=auto -a ./debian/tests/run-unit-test debian/python3-mirtop/usr/share/doc/python3-mirtop chmod -R u\+rw,go=rX debian/python3-mirtop/usr/share/doc install -p -m0644 debian/copyright debian/python3-mirtop/usr/share/doc/python3-mirtop/copyright install -m0755 -d debian/mirtop/usr/share/doc/mirtop install -p -m0644 debian/copyright debian/mirtop/usr/share/doc/mirtop/copyright dh_sphinxdoc -O--buildsystem=pybuild dh_sphinxdoc: warning: Sphinx documentation not found dh_installchangelogs -O--buildsystem=pybuild install -m0755 -d debian/python3-mirtop/usr/share/doc/python3-mirtop install -p -m0644 debian/.debhelper/generated/python3-mirtop/dh_installchangelogs.dch.trimmed debian/python3-mirtop/usr/share/doc/python3-mirtop/changelog.Debian install -p -m0644 ./HISTORY.md debian/python3-mirtop/usr/share/doc/python3-mirtop/changelog install -m0755 -d debian/mirtop/usr/share/doc/mirtop install -p -m0644 debian/.debhelper/generated/mirtop/dh_installchangelogs.dch.trimmed debian/mirtop/usr/share/doc/mirtop/changelog.Debian install -p -m0644 ./HISTORY.md debian/mirtop/usr/share/doc/mirtop/changelog dh_installman -O--buildsystem=pybuild install -m0755 -d debian/mirtop/usr/share/man/man1/ install -p -m0644 ./build/man/mirtop.1 debian/mirtop/usr/share/man/man1/mirtop.1 man-recode --to-code UTF-8 --suffix .dh-new debian/mirtop/usr/share/man/man1/mirtop.1 mv debian/mirtop/usr/share/man/man1/mirtop.1.dh-new debian/mirtop/usr/share/man/man1/mirtop.1 chmod 0644 -- debian/mirtop/usr/share/man/man1/mirtop.1 dh_python3 -O--buildsystem=pybuild D: dh_python3 dh_python3:179: version: 5.20230130 D: dh_python3 dh_python3:180: argv: ['/usr/bin/dh_python3', '-O--buildsystem=pybuild'] D: dh_python3 dh_python3:181: options: Namespace(guess_deps=True, skip_private=False, verbose=True, arch=None, package=None, no_package=None, remaining_packages=False, compile_all=False, vrange=None, regexpr=None, accept_upstream_versions=False, depends=None, depends_section=None, recommends=None, recommends_section=None, suggests=None, suggests_section=None, requires=None, shebang=None, ignore_shebangs=False, clean_dbg_pkg=True, no_ext_rename=False, no_shebang_rewrite=False, private_dir=None, O=['--buildsystem=pybuild']) D: dh_python3 dh_python3:182: supported Python versions: 3.11 (default=3.11) D: dh_python3 debhelper:183: source=mirtop, binary packages=['python3-mirtop', 'mirtop'] D: dh_python3 dh_python3:204: processing package python3-mirtop... D: dh_python3 fs:52: moving files from debian/python3-mirtop/usr/lib/python3.11/dist-packages to debian/python3-mirtop/usr/lib/python3/dist-packages/ D: dh_python3 fs:400: package python3-mirtop details = {'requires.txt': set(), 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': set(), 'public_vers': {Version('3')}, 'private_dirs': {}, 'compile': True, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package python3-mirtop D: dh_python3 depends:281: D={'python3:any'}; R=[]; S=[]; E=[], B=[]; RT=[] D: dh_python3 dh_python3:204: processing package mirtop... D: dh_python3 fs:400: package mirtop details = {'requires.txt': set(), 'egg-info': set(), 'dist-info': set(), 'nsp.txt': set(), 'shebangs': {/usr/bin/python3}, 'public_vers': set(), 'private_dirs': {}, 'compile': False, 'ext_vers': set(), 'ext_no_version': set()} D: dh_python3 depends:117: generating dependencies for package mirtop D: dh_python3 depends:281: D={'python3:any'}; R=[]; S=[]; E=[], B=[]; RT=[] 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 cd debian/python3-mirtop cd debian/mirtop chmod a-x usr/share/doc/mirtop/changelog usr/share/doc/mirtop/changelog.Debian usr/share/man/man1/mirtop.1 chmod a-x usr/share/doc/python3-mirtop/changelog usr/share/doc/python3-mirtop/changelog.Debian gzip -9nf usr/share/doc/python3-mirtop/changelog usr/share/doc/python3-mirtop/changelog.Debian gzip -9nf usr/share/doc/mirtop/changelog usr/share/doc/mirtop/changelog.Debian usr/share/man/man1/mirtop.1 cd '/build/mirtop-0.4.25' cd '/build/mirtop-0.4.25' dh_fixperms -O--buildsystem=pybuild find debian/python3-mirtop ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/mirtop ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/python3-mirtop/usr/share/doc -type f -a -true -a ! -regex 'debian/python3-mirtop/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mirtop/usr/share/doc -type f -a -true -a ! -regex 'debian/mirtop/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mirtop/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mirtop/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/mirtop/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mirtop -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/python3-mirtop/usr/lib -type f -name '*.ali' -a -true -a -true -print0 2>/dev/null | xargs -0r chmod uga-w find debian/mirtop -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/mirtop/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild install -m0755 -d debian/python3-mirtop/DEBIAN printf '#!/bin/sh\nset -e\n' > debian/python3-mirtop/DEBIAN/postinst cat debian/python3-mirtop.postinst.debhelper >> debian/python3-mirtop/DEBIAN/postinst chmod 0755 -- debian/python3-mirtop/DEBIAN/postinst printf '#!/bin/sh\nset -e\n' > debian/python3-mirtop/DEBIAN/prerm cat debian/python3-mirtop.prerm.debhelper >> debian/python3-mirtop/DEBIAN/prerm chmod 0755 -- debian/python3-mirtop/DEBIAN/prerm install -m0755 -d debian/mirtop/DEBIAN dh_gencontrol -O--buildsystem=pybuild install -m0755 -d debian/mirtop/DEBIAN echo misc:Depends= >> debian/mirtop.substvars echo misc:Pre-Depends= >> debian/mirtop.substvars dpkg-gencontrol -pmirtop -ldebian/changelog -Tdebian/mirtop.substvars -Pdebian/mirtop install -m0755 -d debian/python3-mirtop/DEBIAN echo misc:Depends= >> debian/python3-mirtop.substvars echo misc:Pre-Depends= >> debian/python3-mirtop.substvars dpkg-gencontrol -ppython3-mirtop -ldebian/changelog -Tdebian/python3-mirtop.substvars -Pdebian/python3-mirtop dpkg-gencontrol: warning: Depends field of package python3-mirtop: substitution variable ${sphinxdoc:Depends} used, but is not defined chmod 0644 -- debian/python3-mirtop/DEBIAN/control chmod 0644 -- debian/mirtop/DEBIAN/control dh_md5sums -O--buildsystem=pybuild install -m0755 -d debian/mirtop/DEBIAN install -m0755 -d debian/python3-mirtop/DEBIAN cd debian/python3-mirtop >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/mirtop >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/python3-mirtop/DEBIAN/md5sums chmod 0644 -- debian/mirtop/DEBIAN/md5sums dh_builddeb -O--buildsystem=pybuild dpkg-deb --root-owner-group --build debian/python3-mirtop .. dpkg-deb --root-owner-group --build debian/mirtop .. dpkg-deb: building package 'python3-mirtop' in '../python3-mirtop_0.4.25-2_all.deb'. dpkg-deb: building package 'mirtop' in '../mirtop_0.4.25-2_all.deb'. dpkg-genbuildinfo --build=binary -O../mirtop_0.4.25-2_amd64.buildinfo dpkg-genchanges --build=binary -O../mirtop_0.4.25-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from mirtop-0.4.25/debian/source/options: --extend-diff-ignore=^[^/]*[.]egg-info/ 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/4161939/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/4161939/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/4161939 and its subdirectories I: Current time: Thu May 18 09:15:09 +14 2023 I: pbuilder-time-stamp: 1684350909