I: pbuilder: network access will be disabled during build
I: Current time: Tue Jun 11 08:10:52 -12 2024
I: pbuilder-time-stamp: 1718136652
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: using eatmydata during job
I: Copying source file
I: copying [python-pybedtools_0.9.0-4.dsc]
I: copying [./python-pybedtools_0.9.0.orig.tar.gz]
I: copying [./python-pybedtools_0.9.0-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Mon Jan 2 09:28:23 2023 -12
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 ./python-pybedtools_0.9.0-4.dsc: no acceptable signature found
dpkg-source: info: extracting python-pybedtools in python-pybedtools-0.9.0
dpkg-source: info: unpacking python-pybedtools_0.9.0.orig.tar.gz
dpkg-source: info: unpacking python-pybedtools_0.9.0-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying spelling
dpkg-source: info: applying define_filenotfounderror_python2.patch
dpkg-source: info: applying remove_badges_from_documentation.patch
dpkg-source: info: applying add_missing_shebang.patch
dpkg-source: info: applying yaml_safe_load.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/45918/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='935f7e7893c14b929e46a328ac2b259c'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='45918'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.edlZPnBW/pbuilderrc_qXb0 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.edlZPnBW/b1 --logfile b1/build.log python-pybedtools_0.9.0-4.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos6-i386 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 218680 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 22 2023 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 22 2023 more
-rwsr-xr-x 1 root root 58912 Mar 22 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 22 2023 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 2023 tar
-rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 22 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/45918/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: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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, bedtools, cython3, python3-all-dev, python3-setuptools, python3-pysam, python3-matplotlib, python3-pytest, python3-numpy, python3-numpydoc, python3-pandas, python3-psutil, python3-yaml, python3-tk, python3-sphinx, r-base-core, zlib1g-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19604 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 bedtools; however:
Package bedtools is not installed.
pbuilder-satisfydepends-dummy depends on cython3; however:
Package cython3 is not installed.
pbuilder-satisfydepends-dummy depends on python3-all-dev; however:
Package python3-all-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on python3-pysam; however:
Package python3-pysam is not installed.
pbuilder-satisfydepends-dummy depends on python3-matplotlib; however:
Package python3-matplotlib is not installed.
pbuilder-satisfydepends-dummy depends on python3-pytest; however:
Package python3-pytest is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpydoc; however:
Package python3-numpydoc is not installed.
pbuilder-satisfydepends-dummy depends on python3-pandas; however:
Package python3-pandas is not installed.
pbuilder-satisfydepends-dummy depends on python3-psutil; however:
Package python3-psutil is not installed.
pbuilder-satisfydepends-dummy depends on python3-yaml; however:
Package python3-yaml is not installed.
pbuilder-satisfydepends-dummy depends on python3-tk; however:
Package python3-tk is not installed.
pbuilder-satisfydepends-dummy depends on python3-sphinx; however:
Package python3-sphinx is not installed.
pbuilder-satisfydepends-dummy depends on r-base-core; however:
Package r-base-core is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts3{a} libhtscodecs2{a} libice6{a} libicu72{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsm6{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libxt6{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} openssl{a} po-debconf{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-babel{a} python3-beniget{a} python3-brotli{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-docutils{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-idna{a} python3-imagesize{a} python3-iniconfig{a} python3-jinja2{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-pluggy{a} python3-ply{a} python3-psutil{a} python3-py{a} python3-pygments{a} python3-pyparsing{a} python3-pysam{a} python3-pytest{a} python3-pythran{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-yaml{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} r-base-core{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} ucf{a} unicode-data{a} unzip{a} x11-common{a} xdg-utils{a} xml-core{a} zip{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
curl isympy-common javascript-common libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx publicsuffix python3-bottleneck python3-bs4 python3-html5lib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-tables r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs
0 packages upgraded, 212 newly installed, 0 to remove and 0 not upgraded.
Need to get 171 MB of archives. After unpacking 770 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B]
Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 sgml-base all 1.31 [15.4 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 openssl i386 3.0.8-1 [1412 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 ca-certificates all 20230311 [153 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 ucf all 3.0043+nmu1 [55.2 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 bedtools i386 2.30.0+dfsg-3 [734 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libtcl8.6 i386 8.6.13+dfsg-2 [1095 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2 [292 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2 [782 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 libxft2 i386 2.3.6-1 [62.8 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 libtk8.6 i386 8.6.13-2 [824 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-4.1 [622 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 blt i386 2.5.3+dfsg-4.1 [14.9 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 cython3 i386 0.29.32-2+b1 [1297 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 59 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 61 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 70 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB]
Get: 71 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130 [104 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 xml-core all 0.18+nmu1 [23.8 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 docutils-common all 0.19+dfsg-6 [127 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 fontconfig i386 2.14.1-4 [450 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 fonts-lyx all 2.3.7-1 [186 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-20 [9510 kB]
Get: 78 http://deb.debian.org/debian bookworm/main i386 libboost-dev i386 1.74.0.3 [4548 B]
Get: 79 http://deb.debian.org/debian bookworm/main i386 libpixman-1-0 i386 0.42.2-1 [548 kB]
Get: 80 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB]
Get: 81 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB]
Get: 82 http://deb.debian.org/debian bookworm/main i386 libcairo2 i386 1.16.0-7 [627 kB]
Get: 83 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 84 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 85 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 86 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB]
Get: 87 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB]
Get: 88 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB]
Get: 89 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB]
Get: 90 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-9 [412 kB]
Get: 91 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-9 [420 kB]
Get: 92 http://deb.debian.org/debian bookworm/main i386 libdatrie1 i386 0.2.13-2+b1 [45.0 kB]
Get: 93 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB]
Get: 94 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB]
Get: 95 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB]
Get: 96 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB]
Get: 97 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB]
Get: 98 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB]
Get: 99 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB]
Get: 100 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB]
Get: 101 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB]
Get: 102 http://deb.debian.org/debian bookworm/main i386 libice6 i386 2:1.0.10-1 [60.8 kB]
Get: 103 http://deb.debian.org/debian bookworm/main i386 libimagequant0 i386 2.17.0-1 [32.9 kB]
Get: 104 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB]
Get: 105 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB]
Get: 106 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 107 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 108 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 109 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 110 http://deb.debian.org/debian bookworm/main i386 libjson-perl all 4.10000-1 [87.5 kB]
Get: 111 http://deb.debian.org/debian bookworm/main i386 libopenblas0-pthread i386 0.3.21+ds-4 [5148 kB]
Get: 112 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB]
Get: 113 http://deb.debian.org/debian bookworm/main i386 liblbfgsb0 i386 3.0+dfsg.4-1 [28.5 kB]
Get: 114 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB]
Get: 115 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB]
Get: 116 http://deb.debian.org/debian bookworm/main i386 libopenblas0 i386 0.3.21+ds-4 [32.6 kB]
Get: 117 http://deb.debian.org/debian bookworm/main i386 libopenblas-pthread-dev i386 0.3.21+ds-4 [3447 kB]
Get: 118 http://deb.debian.org/debian bookworm/main i386 libopenblas-dev i386 0.3.21+ds-4 [44.9 kB]
Get: 119 http://deb.debian.org/debian bookworm/main i386 libopenjp2-7 i386 2.5.0-1+b1 [196 kB]
Get: 120 http://deb.debian.org/debian bookworm/main i386 libthai-data all 0.1.29-1 [176 kB]
Get: 121 http://deb.debian.org/debian bookworm/main i386 libthai0 i386 0.1.29-1 [58.6 kB]
Get: 122 http://deb.debian.org/debian bookworm/main i386 libpango-1.0-0 i386 1.50.12+ds-1 [220 kB]
Get: 123 http://deb.debian.org/debian bookworm/main i386 libpangoft2-1.0-0 i386 1.50.12+ds-1 [50.5 kB]
Get: 124 http://deb.debian.org/debian bookworm/main i386 libpangocairo-1.0-0 i386 1.50.12+ds-1 [35.4 kB]
Get: 125 http://deb.debian.org/debian bookworm/main i386 libpaper1 i386 1.1.29 [12.7 kB]
Get: 126 http://deb.debian.org/debian bookworm/main i386 libpaper-utils i386 1.1.29 [8972 B]
Get: 127 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB]
Get: 128 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
Get: 129 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB]
Get: 130 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B]
Get: 131 http://deb.debian.org/debian bookworm/main i386 libpython3-all-dev i386 3.11.2-1+b1 [1068 B]
Get: 132 http://deb.debian.org/debian bookworm/main i386 libqhull-r8.0 i386 2020.2-5 [260 kB]
Get: 133 http://deb.debian.org/debian bookworm/main i386 libraqm0 i386 0.7.0-4.1 [11.1 kB]
Get: 134 http://deb.debian.org/debian bookworm/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB]
Get: 135 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.1 [293 kB]
Get: 136 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-5 [332 kB]
Get: 137 http://deb.debian.org/debian bookworm/main i386 libwebpdemux2 i386 1.2.4-0.1 [99.7 kB]
Get: 138 http://deb.debian.org/debian bookworm/main i386 libwebpmux3 i386 1.2.4-0.1 [111 kB]
Get: 139 http://deb.debian.org/debian bookworm/main i386 libxsimd-dev i386 8.1.0-7 [88.8 kB]
Get: 140 http://deb.debian.org/debian bookworm/main i386 libxslt1.1 i386 1.1.35-1 [253 kB]
Get: 141 http://deb.debian.org/debian bookworm/main i386 libxt6 i386 1:1.2.1-1.1 [192 kB]
Get: 142 http://deb.debian.org/debian bookworm/main i386 libyaml-0-2 i386 0.2.5-1 [55.9 kB]
Get: 143 http://deb.debian.org/debian bookworm/main i386 python-babel-localedata all 2.10.3-1 [5615 kB]
Get: 144 http://deb.debian.org/debian bookworm/main i386 python-matplotlib-data all 3.6.3-1 [2744 kB]
Get: 145 http://deb.debian.org/debian bookworm/main i386 python3-alabaster all 0.7.12-1 [20.8 kB]
Get: 146 http://deb.debian.org/debian bookworm/main i386 python3-all i386 3.11.2-1+b1 [1056 B]
Get: 147 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB]
Get: 148 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB]
Get: 149 http://deb.debian.org/debian bookworm/main i386 python3-all-dev i386 3.11.2-1+b1 [1072 B]
Get: 150 http://deb.debian.org/debian bookworm/main i386 python3-appdirs all 1.4.4-3 [13.0 kB]
Get: 151 http://deb.debian.org/debian bookworm/main i386 python3-attr all 22.2.0-1 [65.4 kB]
Get: 152 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 153 http://deb.debian.org/debian bookworm/main i386 python3-tz all 2022.7.1-3 [30.1 kB]
Get: 154 http://deb.debian.org/debian bookworm/main i386 python3-babel all 2.10.3-1 [103 kB]
Get: 155 http://deb.debian.org/debian bookworm/main i386 python3-gast all 0.5.2-2 [9364 B]
Get: 156 http://deb.debian.org/debian bookworm/main i386 python3-beniget all 0.4.1-3 [9920 B]
Get: 157 http://deb.debian.org/debian bookworm/main i386 python3-brotli i386 1.0.9-2+b6 [295 kB]
Get: 158 http://deb.debian.org/debian bookworm/main i386 python3-certifi all 2022.9.24-1 [153 kB]
Get: 159 http://deb.debian.org/debian bookworm/main i386 python3-chardet all 5.1.0+dfsg-2 [110 kB]
Get: 160 http://deb.debian.org/debian bookworm/main i386 python3-charset-normalizer all 3.0.1-2 [49.3 kB]
Get: 161 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB]
Get: 162 http://deb.debian.org/debian bookworm/main i386 python3-contourpy i386 1.0.7-1+b1 [184 kB]
Get: 163 http://deb.debian.org/debian bookworm/main i386 python3-cycler all 0.11.0-1 [8020 B]
Get: 164 http://deb.debian.org/debian bookworm/main i386 python3-six all 1.16.0-4 [17.5 kB]
Get: 165 http://deb.debian.org/debian bookworm/main i386 python3-dateutil all 2.8.2-2 [78.3 kB]
Get: 166 http://deb.debian.org/debian bookworm/main i386 python3-decorator all 5.1.1-3 [14.9 kB]
Get: 167 http://deb.debian.org/debian bookworm/main i386 python3-roman all 3.3-3 [9880 B]
Get: 168 http://deb.debian.org/debian bookworm/main i386 python3-docutils all 0.19+dfsg-6 [382 kB]
Get: 169 http://deb.debian.org/debian bookworm/main i386 python3-ply all 3.11-5 [65.8 kB]
Get: 170 http://deb.debian.org/debian bookworm/main i386 python3-pythran i386 0.11.0+ds-7 [427 kB]
Get: 171 http://deb.debian.org/debian bookworm/main i386 python3-scipy i386 1.10.1-2 [15.2 MB]
Get: 172 http://deb.debian.org/debian bookworm/main i386 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB]
Get: 173 http://deb.debian.org/debian bookworm/main i386 python3-mpmath all 1.2.1-2 [418 kB]
Get: 174 http://deb.debian.org/debian bookworm/main i386 python3-sympy all 1.11.1-1 [4358 kB]
Get: 175 http://deb.debian.org/debian bookworm/main i386 python3-fs all 2.4.16-2 [95.2 kB]
Get: 176 http://deb.debian.org/debian bookworm/main i386 python3-lxml i386 4.9.2-1+b1 [1182 kB]
Get: 177 http://deb.debian.org/debian bookworm/main i386 python3-lz4 i386 4.0.2+dfsg-1+b2 [25.1 kB]
Get: 178 http://deb.debian.org/debian bookworm/main i386 unicode-data all 15.0.0-1 [7984 kB]
Get: 179 http://deb.debian.org/debian bookworm/main i386 python3-fonttools i386 4.38.0-1+b1 [1010 kB]
Get: 180 http://deb.debian.org/debian bookworm/main i386 python3-idna all 3.3-1 [39.4 kB]
Get: 181 http://deb.debian.org/debian bookworm/main i386 python3-imagesize all 1.4.1-1 [6688 B]
Get: 182 http://deb.debian.org/debian bookworm/main i386 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 183 http://deb.debian.org/debian bookworm/main i386 python3-markupsafe i386 2.1.2-1+b1 [13.3 kB]
Get: 184 http://deb.debian.org/debian bookworm/main i386 python3-jinja2 all 3.1.2-1 [119 kB]
Get: 185 http://deb.debian.org/debian bookworm/main i386 python3-kiwisolver i386 1.4.4-1+b1 [63.0 kB]
Get: 186 http://deb.debian.org/debian bookworm/main i386 python3-pil i386 9.4.0-1.1+b1 [473 kB]
Get: 187 http://deb.debian.org/debian bookworm/main i386 python3-tk i386 3.11.2-3 [99.2 kB]
Get: 188 http://deb.debian.org/debian bookworm/main i386 python3-pil.imagetk i386 9.4.0-1.1+b1 [74.7 kB]
Get: 189 http://deb.debian.org/debian bookworm/main i386 python3-pyparsing all 3.0.9-1 [138 kB]
Get: 190 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB]
Get: 191 http://deb.debian.org/debian bookworm/main i386 python3-matplotlib i386 3.6.3-1+b1 [6891 kB]
Get: 192 http://deb.debian.org/debian bookworm/main i386 python3-more-itertools all 8.10.0-2 [53.0 kB]
Get: 193 http://deb.debian.org/debian bookworm/main i386 sphinx-common all 5.3.0-4 [653 kB]
Get: 194 http://deb.debian.org/debian bookworm/main i386 python3-pygments all 2.14.0+dfsg-1 [783 kB]
Get: 195 http://deb.debian.org/debian bookworm/main i386 python3-urllib3 all 1.26.12-1 [117 kB]
Get: 196 http://deb.debian.org/debian bookworm/main i386 python3-requests all 2.28.1+dfsg-1 [67.9 kB]
Get: 197 http://deb.debian.org/debian bookworm/main i386 python3-snowballstemmer all 2.2.0-2 [57.8 kB]
Get: 198 http://deb.debian.org/debian bookworm/main i386 python3-sphinx all 5.3.0-4 [549 kB]
Get: 199 http://deb.debian.org/debian bookworm/main i386 python3-numpydoc all 1.5.0-1 [43.0 kB]
Get: 200 http://deb.debian.org/debian bookworm/main i386 python3-pandas-lib i386 1.5.3+dfsg-2 [3382 kB]
Get: 201 http://deb.debian.org/debian bookworm/main i386 python3-pandas all 1.5.3+dfsg-2 [2885 kB]
Get: 202 http://deb.debian.org/debian bookworm/main i386 python3-pluggy all 1.0.0+repack-1 [19.7 kB]
Get: 203 http://deb.debian.org/debian bookworm/main i386 python3-psutil i386 5.9.4-1+b1 [190 kB]
Get: 204 http://deb.debian.org/debian bookworm/main i386 python3-py all 1.11.0-1 [89.2 kB]
Get: 205 http://deb.debian.org/debian bookworm/main i386 python3-pysam i386 0.20.0+ds-3+b1 [1708 kB]
Get: 206 http://deb.debian.org/debian bookworm/main i386 python3-pytest all 7.2.1-2 [236 kB]
Get: 207 http://deb.debian.org/debian bookworm/main i386 python3-setuptools all 66.1.1-1 [521 kB]
Get: 208 http://deb.debian.org/debian bookworm/main i386 python3-yaml i386 6.0-3+b2 [119 kB]
Get: 209 http://deb.debian.org/debian bookworm/main i386 zip i386 3.0-13 [236 kB]
Get: 210 http://deb.debian.org/debian bookworm/main i386 unzip i386 6.0-28 [166 kB]
Get: 211 http://deb.debian.org/debian bookworm/main i386 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get: 212 http://deb.debian.org/debian bookworm/main i386 r-base-core i386 4.2.2.20221110-2 [26.1 MB]
Fetched 171 MB in 5s (31.4 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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invoke-rc.d: could not determine current runlevel
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Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up libopenblas0:i386 (0.3.21+ds-4) ...
Setting up groff-base (1.22.4-10) ...
Setting up xml-core (0.18+nmu1) ...
Setting up libxslt1.1:i386 (1.1.35-1) ...
Setting up libcurl4:i386 (7.88.1-9) ...
Setting up libx11-6:i386 (2:1.8.4-2) ...
Setting up libharfbuzz0b:i386 (6.0.0+dfsg-3) ...
Setting up libfontconfig1:i386 (2.14.1-4) ...
Setting up libsm6:i386 (2:1.2.3-1) ...
Setting up liblbfgsb0:i386 (3.0+dfsg.4-1) ...
Setting up libopenblas-pthread-dev:i386 (0.3.21+ds-4) ...
update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode
update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode
update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/i386-linux-gnu/libopenblas.so (libopenblas.so-i386-linux-gnu) in auto mode
Setting up libpaper1:i386 (1.1.29) ...
Creating config file /etc/papersize with new version
Setting up fontconfig (2.14.1-4) ...
Regenerating fonts cache... done.
Setting up libxrender1:i386 (1:0.9.10-1.1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpython3.11-stdlib:i386 (3.11.2-6) ...
Setting up libpango-1.0-0:i386 (1.50.12+ds-1) ...
Setting up libxext6:i386 (2:1.3.4-1+b1) ...
Setting up libcurl3-gnutls:i386 (7.88.1-9) ...
Setting up libpaper-utils (1.1.29) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:i386 (1.16.0-7) ...
Setting up libopenblas-dev:i386 (0.3.21+ds-4) ...
Setting up libraqm0:i386 (0.7.0-4.1) ...
Setting up sphinx-common (5.3.0-4) ...
Setting up libxt6:i386 (1:1.2.1-1.1) ...
Setting up libxss1:i386 (1:1.2.3-1) ...
Setting up libpangoft2-1.0-0:i386 (1.50.12+ds-1) ...
Setting up libpangocairo-1.0-0:i386 (1.50.12+ds-1) ...
Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ...
Setting up python3.11 (3.11.2-6) ...
Setting up libxft2:i386 (2.3.6-1) ...
Setting up libhts3:i386 (1.16+ds-3) ...
Setting up libpython3.11:i386 (3.11.2-6) ...
Setting up libtk8.6:i386 (8.6.13-2) ...
Setting up debhelper (13.11.4) ...
Setting up python3 (3.11.2-1+b1) ...
Setting up python3-markupsafe (2.1.2-1+b1) ...
Setting up python3-psutil (5.9.4-1+b1) ...
Setting up python3-tz (2022.7.1-3) ...
Setting up python3-six (1.16.0-4) ...
Setting up python3-roman (3.3-3) ...
Setting up python3-decorator (5.1.1-3) ...
Setting up python3-jinja2 (3.1.2-1) ...
Setting up python3-packaging (23.0-1) ...
Setting up python3-pyparsing (3.0.9-1) ...
Setting up python3-certifi (2022.9.24-1) ...
Setting up python3-snowballstemmer (2.2.0-2) ...
Setting up libpython3.11-dev:i386 (3.11.2-6) ...
Setting up python3-brotli (1.0.9-2+b6) ...
Setting up python3-cycler (0.11.0-1) ...
Setting up r-base-core (4.2.2.20221110-2) ...
Creating config file /etc/R/Renviron with new version
Setting up python3-kiwisolver (1.4.4-1+b1) ...
Setting up python3-idna (3.3-1) ...
Setting up cython3 (0.29.32-2+b1) ...
Setting up python3-urllib3 (1.26.12-1) ...
Setting up python3-pluggy (1.0.0+repack-1) ...
Setting up python3-lxml:i386 (4.9.2-1+b1) ...
Setting up python3-dateutil (2.8.2-2) ...
Setting up python3-mpmath (1.2.1-2) ...
Setting up python3-lib2to3 (3.11.2-3) ...
Setting up python3-appdirs (1.4.4-3) ...
Setting up python3-imagesize (1.4.1-1) ...
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-more-itertools (8.10.0-2) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-sympy (1.11.1-1) ...
Setting up python3-attr (22.2.0-1) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Setting up python3-pysam (0.20.0+ds-3+b1) ...
Setting up libpython3-dev:i386 (3.11.2-1+b1) ...
Setting up python3-setuptools (66.1.1-1) ...
Setting up python3-py (1.11.0-1) ...
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-lz4 (4.0.2+dfsg-1+b2) ...
Setting up python3.11-dev (3.11.2-6) ...
Setting up python3-charset-normalizer (3.0.1-2) ...
Setting up python3-pytest (7.2.1-2) ...
Setting up python3-alabaster (0.7.12-1) ...
Setting up blt (2.5.3+dfsg-4.1) ...
Setting up python3-ply (3.11-5) ...
Setting up python3-gast (0.5.2-2) ...
Setting up python3-all (3.11.2-1+b1) ...
Setting up python3-yaml (6.0-3+b2) ...
Setting up python3-tk:i386 (3.11.2-3) ...
Setting up python3-fs (2.4.16-2) ...
Setting up python3-beniget (0.4.1-3) ...
Setting up python3-pygments (2.14.0+dfsg-1) ...
Setting up python3-chardet (5.1.0+dfsg-2) ...
Setting up libpython3-all-dev:i386 (3.11.2-1+b1) ...
Setting up python3-dev (3.11.2-1+b1) ...
Setting up python3-requests (2.28.1+dfsg-1) ...
Setting up python3-numpy (1:1.24.2-1) ...
Setting up python3-contourpy (1.0.7-1+b1) ...
Setting up python3-all-dev (3.11.2-1+b1) ...
Setting up python3-pandas-lib:i386 (1.5.3+dfsg-2) ...
Setting up python3-pandas (1.5.3+dfsg-2) ...
Setting up python3-pythran (0.11.0+ds-7) ...
Setting up python3-scipy (1.10.1-2) ...
Setting up python3-pil:i386 (9.4.0-1.1+b1) ...
Setting up python3-pil.imagetk:i386 (9.4.0-1.1+b1) ...
Setting up python3-ufolib2 (0.14.0+dfsg1-1) ...
Setting up python3-fonttools (4.38.0-1+b1) ...
Setting up python3-matplotlib (3.6.3-1+b1) ...
Processing triggers for libc-bin (2.36-9) ...
Processing triggers for sgml-base (1.31) ...
Setting up docutils-common (0.19+dfsg-6) ...
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-numpydoc (1.5.0-1) ...
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
I: Building the package
I: Running cd /build/python-pybedtools-0.9.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pybedtools_0.9.0-4_source.changes
dpkg-buildpackage: info: source package python-pybedtools
dpkg-buildpackage: info: source version 0.9.0-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/python-pybedtools-0.9.0'
/bin/rm -rf fakehome .eggs .pybuild
/bin/rm -rf debian/python3-pybedtools debian/files
/bin/rm -rf pybedtools.egg-info
/bin/rm -rf pybedtools/scripts/__pycache__/
/bin/rm -rf pybedtools/contrib/__pycache__/
/bin/rm -rf pybedtools/__pycache__/
find pybedtools -name "*.so" -o -name "*.o" | xargs -r rm
rm -rf build
/bin/rm -rf pybedtools/cbedtools.cpp pybedtools/featurefuncs.cpp
find docs/source/autodocs/ -name "*.rst" | xargs -r /bin/rm
# dh_auto_clean
make[1]: Leaving directory '/build/python-pybedtools-0.9.0'
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
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
I: pybuild base:240: python3.11 setup.py config
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/python-pybedtools-0.9.0'
python3 setup.py cythonize
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
running cythonize
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pybedtools-0.9.0/pybedtools/cbedtools.pxd
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/python-pybedtools-0.9.0/pybedtools/featurefuncs.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling pybedtools/cbedtools.pyx because it changed.
Compiling pybedtools/featurefuncs.pyx because it changed.
[1/2] Cythonizing pybedtools/cbedtools.pyx
[2/2] Cythonizing pybedtools/featurefuncs.pyx
dh_auto_build
I: pybuild base:240: /usr/bin/python3 setup.py build
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
running build
running build_py
creating /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/genome_registry.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/helpers.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/parallel.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/logger.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/version.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/stats.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/__init__.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/settings.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/bedtool.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/paths.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/filenames.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
creating /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_1.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_len_leak.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_iter.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_contrib.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_issues.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_pathlib.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_helpers.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/tfuncs.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/__init__.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/regression_tests.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
creating /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
creating /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
running egg_info
creating pybedtools.egg-info
writing pybedtools.egg-info/PKG-INFO
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pybedtools'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pybedtools.include' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'pybedtools.include' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'pybedtools.include' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'pybedtools.include' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
copying pybedtools/_Window.pyx -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/cbedtools.cpp -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/cbedtools.pxd -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/cbedtools.pyx -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/featurefuncs.cpp -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/featurefuncs.pyx -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
creating /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/bedFile.cpp -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/bedFile.h -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/fileType.cpp -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/fileType.h -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/gzstream.cpp -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/gzstream.h -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/test/data/mm9.bed12 -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/small.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/x.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/b.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test.fa -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/c.gff -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/x.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/y.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/d.gff -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/mpl-expected.png -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_cases.yaml -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
INFO: C compiler: i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pybedtools-0.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
creating build
creating build/temp.linux-i386-cpython-311
creating build/temp.linux-i386-cpython-311/pybedtools
creating build/temp.linux-i386-cpython-311/pybedtools/include
INFO: compile options: '-Ipybedtools/include/ -I/usr/include/python3.11 -c'
INFO: i686-linux-gnu-gcc: pybedtools/cbedtools.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/bedFile.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/fileType.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/gzstream.cpp
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function 'BIN getBin(CHRPOS, CHRPOS)':
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from pybedtools/cbedtools.cpp:796:
pybedtools/include/bedFile.h: In function 'BIN getBin(CHRPOS, CHRPOS)':
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pybedtools-0.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pybedtools/cbedtools.o build/temp.linux-i386-cpython-311/pybedtools/include/bedFile.o build/temp.linux-i386-cpython-311/pybedtools/include/fileType.o build/temp.linux-i386-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.cpython-311-i386-linux-gnu.so
building 'pybedtools.featurefuncs' extension
INFO: C compiler: i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pybedtools-0.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
INFO: compile options: '-Ipybedtools/include/ -I/usr/include/python3.11 -c'
INFO: i686-linux-gnu-gcc: pybedtools/include/bedFile.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/fileType.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/gzstream.cpp
INFO: i686-linux-gnu-gcc: pybedtools/featurefuncs.cpp
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function 'BIN getBin(CHRPOS, CHRPOS)':
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from pybedtools/featurefuncs.cpp:796:
pybedtools/include/bedFile.h: In function 'BIN getBin(CHRPOS, CHRPOS)':
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pybedtools-0.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i386-cpython-311/pybedtools/featurefuncs.o build/temp.linux-i386-cpython-311/pybedtools/include/bedFile.o build/temp.linux-i386-cpython-311/pybedtools/include/fileType.o build/temp.linux-i386-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.cpython-311-i386-linux-gnu.so
python3 setup.py develop --user
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
running develop
/usr/lib/python3/dist-packages/setuptools/command/easy_install.py:146: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
/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 egg_info
writing pybedtools.egg-info/PKG-INFO
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pybedtools'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
running build_ext
building 'pybedtools.cbedtools' extension
INFO: C compiler: i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pybedtools-0.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/pybedtools
creating build/temp.linux-x86_64-cpython-311/pybedtools/include
INFO: compile options: '-Ipybedtools/include/ -I/usr/include/python3.11 -c'
INFO: i686-linux-gnu-gcc: pybedtools/cbedtools.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/bedFile.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/fileType.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/gzstream.cpp
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function 'BIN getBin(CHRPOS, CHRPOS)':
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from pybedtools/cbedtools.cpp:796:
pybedtools/include/bedFile.h: In function 'BIN getBin(CHRPOS, CHRPOS)':
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pybedtools-0.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-311/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-311/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o /build/python-pybedtools-0.9.0/pybedtools/cbedtools.cpython-311-i386-linux-gnu.so
building 'pybedtools.featurefuncs' extension
INFO: C compiler: i686-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/python-pybedtools-0.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
INFO: compile options: '-Ipybedtools/include/ -I/usr/include/python3.11 -c'
INFO: i686-linux-gnu-gcc: pybedtools/include/bedFile.cpp
INFO: i686-linux-gnu-gcc: pybedtools/featurefuncs.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/gzstream.cpp
INFO: i686-linux-gnu-gcc: pybedtools/include/fileType.cpp
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function 'BIN getBin(CHRPOS, CHRPOS)':
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
In file included from pybedtools/featurefuncs.cpp:796:
pybedtools/include/bedFile.h: In function 'BIN getBin(CHRPOS, CHRPOS)':
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
INFO: i686-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/python-pybedtools-0.9.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-311/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-311/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o /build/python-pybedtools-0.9.0/pybedtools/featurefuncs.cpython-311-i386-linux-gnu.so
Creating /build/python-pybedtools-0.9.0/fakehome/.local/lib/python3.11/site-packages/pybedtools.egg-link (link to .)
Adding pybedtools 0.9.0 to easy-install.pth file
Installed /build/python-pybedtools-0.9.0
Processing dependencies for pybedtools==0.9.0
Searching for six==1.16.0
Best match: six 1.16.0
Adding six 1.16.0 to easy-install.pth file
Using /usr/lib/python3/dist-packages
Searching for pysam==0.20.0
Best match: pysam 0.20.0
Adding pysam 0.20.0 to easy-install.pth file
Using /usr/lib/python3/dist-packages
Finished processing dependencies for pybedtools==0.9.0
python3 setup.py build_sphinx
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
running build_sphinx
Running Sphinx v5.3.0
making output directory... done
[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst
generated new fontManager
[autosummary] generating autosummary for: /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst, /build/python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.add_color.rst, /build/python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst, /build/python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.extend_fields.rst, /build/python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.five_prime.rst, /build/python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.greater_than.rst, /build/python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.less_than.rst, /build/python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst, /build/python-pybedtools-0.9.0/docs/source/pybedtools.featurefuncs.three_prime.rst
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/usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/python-pybedtools-0.9.0/pybedtools/contrib/long_range_interaction.py.
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/build/python-pybedtools-0.9.0/docs/source/autodocs/pybedtools.contrib.plotting.Track.rst:155: WARNING: autosummary: failed to import Track.colorbar.
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/build/python-pybedtools-0.9.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy<https://github.com/vanheeringen-lab/genomepy/>".
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writing output... [ 83%] pybedtools.featurefuncs.bedgraph_scale
writing output... [ 84%] pybedtools.featurefuncs.center
writing output... [ 84%] pybedtools.featurefuncs.extend_fields
writing output... [ 85%] pybedtools.featurefuncs.five_prime
writing output... [ 85%] pybedtools.featurefuncs.gff2bed
writing output... [ 86%] pybedtools.featurefuncs.greater_than
writing output... [ 87%] pybedtools.featurefuncs.less_than
writing output... [ 87%] pybedtools.featurefuncs.midpoint
writing output... [ 88%] pybedtools.featurefuncs.normalized_to_length
writing output... [ 89%] pybedtools.featurefuncs.rename
writing output... [ 89%] pybedtools.featurefuncs.three_prime
writing output... [ 90%] save-results
writing output... [ 91%] scripts
writing output... [ 91%] sh-comparison
writing output... [ 92%] topical-bam
writing output... [ 92%] topical-bam-semantics
writing output... [ 93%] topical-comparisons
writing output... [ 94%] topical-create-a-bedtool
writing output... [ 94%] topical-design-principles
writing output... [ 95%] topical-documentation-contents
writing output... [ 96%] topical-genome
writing output... [ 96%] topical-iterators
writing output... [ 97%] topical-low-level-ops
writing output... [ 98%] topical-random
writing output... [ 98%] topical-saving
writing output... [ 99%] topical-wrapping
writing output... [100%] tutorial-contents
/build/python-pybedtools-0.9.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history.<locals>.decorated:9: WARNING: Could not lex literal_block as "python". Highlighting skipped.
/build/python-pybedtools-0.9.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history.<locals>.decorated:28: WARNING: Could not lex literal_block as "python". Highlighting skipped.
/build/python-pybedtools-0.9.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history.<locals>.decorated:20: WARNING: Could not lex literal_block as "python". Highlighting skipped.
/build/python-pybedtools-0.9.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history.<locals>.decorated:16: WARNING: Could not lex literal_block as "python". Highlighting skipped.
/build/python-pybedtools-0.9.0/docs/source/default-arguments.rst:35: WARNING: Could not lex literal_block as "python". Highlighting skipped.
/build/python-pybedtools-0.9.0/docs/source/topical-design-principles.rst:120: WARNING: unknown option: 'mergeBed -i'
/build/python-pybedtools-0.9.0/docs/source/topical-design-principles.rst:127: WARNING: unknown option: '-i'
generating indices... genindex py-modindex done
highlighting module code... [ 7%] pybedtools
highlighting module code... [ 15%] pybedtools.bedtool
highlighting module code... [ 23%] pybedtools.cbedtools
highlighting module code... [ 30%] pybedtools.contrib.bigbed
highlighting module code... [ 38%] pybedtools.contrib.bigwig
highlighting module code... [ 46%] pybedtools.contrib.intersection_matrix
highlighting module code... [ 53%] pybedtools.contrib.long_range_interaction
highlighting module code... [ 61%] pybedtools.contrib.plotting
highlighting module code... [ 69%] pybedtools.contrib.venn_maker
highlighting module code... [ 76%] pybedtools.featurefuncs
highlighting module code... [ 84%] pybedtools.filenames
highlighting module code... [ 92%] pybedtools.helpers
highlighting module code... [100%] pybedtools.parallel
writing additional pages... search done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 9 warnings.
The HTML pages are in build/sphinx/html.
make[1]: Leaving directory '/build/python-pybedtools-0.9.0'
dh_auto_test -O--buildsystem=pybuild
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
dh_installdirs -O--buildsystem=pybuild
dh_auto_install -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/python-pybedtools-0.9.0/debian/python3-pybedtools
/usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
if not hasattr(numpy, method):
/usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
obj = getattr(themodule, elem)
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 pybedtools/version.py -> /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
running egg_info
writing pybedtools.egg-info/PKG-INFO
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pybedtools'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'pybedtools.include' as data is deprecated, please list it in `packages`.
!!
############################
# Package would be ignored #
############################
Python recognizes 'pybedtools.include' as an importable package,
but it is not listed in the `packages` configuration of setuptools.
'pybedtools.include' has been automatically added to the distribution only
because it may contain data files, but this behavior is likely to change
in future versions of setuptools (and therefore is considered deprecated).
Please make sure that 'pybedtools.include' is included as a package by using
the `packages` configuration field or the proper discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" and "data files" on setuptools
documentation page.
!!
check.warn(importable)
running build_ext
running install_lib
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/intersection_matrix.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/venn_maker.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/plotting.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/long_range_interaction.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/__init__.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/bigbed.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/bigwig.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/genome_registry.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.cpp -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.pyx -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/helpers.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/parallel.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.cpython-311-i386-linux-gnu.so -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.cpp -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/gzstream.h -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/lineFileUtilities.h -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/bedFile.h -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/bedFile.cpp -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/gzstream.cpp -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/fileType.cpp -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/fileType.h -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.cpython-311-i386-linux-gnu.so -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_1.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_len_leak.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_iter.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_gzip_support.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_merge215.yaml -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/mpl-expected.png -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_merge227.yaml -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_shuffle227.yaml -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
creating /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/mm9.bed12 -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/bedpe.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.gff -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.sorted.bam.bai -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/snps.bed.gz -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/small.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/venn.c.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/expand_test.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/reads.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test.fa.fai -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.othersort.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/m1.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test_tsses.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/hg38-problem.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/x.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/genome.fa -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/b.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/164.gtf -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.1.100.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/vcf-stderr-test.vcf -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/tag_test1.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/1000genomes-example.vcf -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/issue_121.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test.fa -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/c.gff -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test_bedpe.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/democonfig.yaml -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/hg19.gff -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/hg38-base.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/small.fastq -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/v.vcf -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/a.igv_script -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.sorted.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.50.200.bam.bai -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/issue319.out.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.gff.gz -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/venn.b.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/x.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.1.100.bam.bai -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.50.200.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/a.links.html -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/y.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.cram -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/exons.gff -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test_peaks.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/bedpe2.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/__init__.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.bam -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/issue319.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/multibamcov_test.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/a.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/tag_test2.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/vcf-stderr-test.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/d.gff -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/issue319.vcf.gz -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_contrib.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_cases.yaml -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_issues.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/gchart-expected.png -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_pathlib.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_helpers.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/tfuncs.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/prevent_open_file_regression -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__init__.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/genomepy_integration.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/regression_tests.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_shuffle215.yaml -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_cbedtools.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/logger.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/version.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/_Window.pyx -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/stats.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__init__.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.pxd -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/settings.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/bedtool.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/paths.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/filenames.py -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /build/python-pybedtools-0.9.0/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.pyx -> /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/intersection_matrix.py to intersection_matrix.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/venn_maker.py to venn_maker.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/plotting.py to plotting.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/long_range_interaction.py to long_range_interaction.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/bigbed.py to bigbed.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/bigwig.py to bigwig.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/genome_registry.py to genome_registry.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/helpers.py to helpers.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/parallel.py to parallel.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_1.py to test_1.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_len_leak.py to test_len_leak.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_iter.py to test_iter.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_gzip_support.py to test_gzip_support.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_contrib.py to test_contrib.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_issues.py to test_issues.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_pathlib.py to test_pathlib.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_helpers.py to test_helpers.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/tfuncs.py to tfuncs.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/genomepy_integration.py to genomepy_integration.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/regression_tests.py to regression_tests.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_cbedtools.py to test_cbedtools.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/logger.py to logger.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/version.py to version.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/stats.py to stats.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/settings.py to settings.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/bedtool.py to bedtool.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/paths.py to paths.cpython-311.pyc
byte-compiling /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/filenames.py to filenames.cpython-311.pyc
running install_egg_info
Copying pybedtools.egg-info to /build/python-pybedtools-0.9.0/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools-0.9.0.egg-info
Skipping SOURCES.txt
running install_scripts
debian/rules override_dh_install
make[1]: Entering directory '/build/python-pybedtools-0.9.0'
dh_install
rm -f debian/python3-pybedtools/usr/lib/python3*/dist-packages/pybedtools/test/prevent_open_file_regression
make[1]: Leaving directory '/build/python-pybedtools-0.9.0'
dh_installdocs -O--buildsystem=pybuild
dh_installdocs: warning: Cannot auto-detect main package for python-pybedtools-doc. If the default is wrong, please use --doc-main-package
dh_sphinxdoc -O--buildsystem=pybuild
dh_installchangelogs -O--buildsystem=pybuild
dh_installexamples -O--buildsystem=pybuild
dh_installexamples: warning: Cannot auto-detect main package for python-pybedtools-doc. If the default is wrong, please use --doc-main-package
dh_python3 -O--buildsystem=pybuild
dh_installsystemduser -O--buildsystem=pybuild
dh_perl -O--buildsystem=pybuild
dh_link -O--buildsystem=pybuild
dh_strip_nondeterminism -O--buildsystem=pybuild
dh_compress -O--buildsystem=pybuild
dh_fixperms -O--buildsystem=pybuild
dh_missing -O--buildsystem=pybuild
dh_dwz -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -O--buildsystem=pybuild
dh_gencontrol -O--buildsystem=pybuild
dpkg-gencontrol: warning: Depends field of package pybedtools-bin: substitution variable ${python3:Depends} used, but is not defined
dh_md5sums -O--buildsystem=pybuild
dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'pybedtools-bin' in '../pybedtools-bin_0.9.0-4_all.deb'.
dpkg-deb: building package 'python3-pybedtools' in '../python3-pybedtools_0.9.0-4_i386.deb'.
dpkg-deb: building package 'python3-pybedtools-dbgsym' in '../python3-pybedtools-dbgsym_0.9.0-4_i386.deb'.
dpkg-deb: building package 'python-pybedtools-doc' in '../python-pybedtools-doc_0.9.0-4_all.deb'.
dpkg-genbuildinfo --build=binary -O../python-pybedtools_0.9.0-4_i386.buildinfo
dpkg-genchanges --build=binary -O../python-pybedtools_0.9.0-4_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: 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/45918 and its subdirectories
I: Current time: Tue Jun 11 08:13:09 -12 2024
I: pbuilder-time-stamp: 1718136789