I: pbuilder: network access will be disabled during build
I: Current time: Tue Dec 31 13:00:08 +14 2024
I: pbuilder-time-stamp: 1735599608
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [python-pybedtools_0.10.0-4.dsc]
I: copying [./python-pybedtools_0.10.0.orig.tar.xz]
I: copying [./python-pybedtools_0.10.0-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Dec 27 01:57:35 2024 
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv:                issuer "crusoe@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.10.0-4.dsc: no acceptable signature found
dpkg-source: info: extracting python-pybedtools in python-pybedtools-0.10.0
dpkg-source: info: unpacking python-pybedtools_0.10.0.orig.tar.xz
dpkg-source: info: unpacking python-pybedtools_0.10.0-4.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
dpkg-source: info: applying 416.patch
dpkg-source: info: applying fix-doctest-imports.py
dpkg-source: info: applying doc-build-no-special-path
dpkg-source: info: applying test-tempdir
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/12153/tmp/hooks/D01_modify_environment starting
debug: Running on ff4a.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Dec 30 23:00 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/12153/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/12153/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
  BASH_VERSION='5.2.37(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=armhf
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 '
  DIRSTACK=()
  DISTRIBUTION=trixie
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=arm
  HOST_ARCH=armhf
  IFS=' 	
  '
  INVOCATION_ID=40e79a28a1c24e19ba73679439f71c94
  LANG=C
  LANGUAGE=it_CH:it
  LC_ALL=C
  MACHTYPE=arm-unknown-linux-gnueabihf
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnueabihf
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=12153
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.71di5CVi/pbuilderrc_PbSu --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.71di5CVi/b2 --logfile b2/build.log python-pybedtools_0.10.0-4.dsc'
  SUDO_GID=113
  SUDO_UID=107
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://10.0.0.15:3142/
I: uname -a
  Linux i-capture-the-hostname 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/12153/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: armhf
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-sequence-python3, pybuild-plugin-pyproject, bedtools, cython3, python3-all-dev, python3-setuptools, python3-pysam, python3-matplotlib, python3-pytest, python3-numpy, python3-numpydoc, python3-pandas, python3-psutil, python3-yaml, 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 ... 19680 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however:
  Package dh-sequence-python3 is not installed.
 pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however:
  Package pybuild-plugin-pyproject 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-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-dejavu-mono{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{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} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libopenjp2-7{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{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} libxslt1.1{a} libxss1{a} libxt6t64{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-brotli{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-fonttools{a} python3-fs{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-kiwisolver{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-platformdirs{a} python3-pluggy{a} python3-psutil{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pysam{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sympy{a} python3-tabulate{a} python3-tk{a} python3-toml{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-wheel{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} r-base-core{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} tzdata{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 krb5-locales 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 linux-sysctl-defaults lynx psmisc publicsuffix python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch 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, 238 newly installed, 0 to remove and 0 not upgraded.
Need to get 169 MB of archives. After unpacking 646 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main armhf libpython3.12-minimal armhf 3.12.8-3 [802 kB]
Get: 2 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB]
Get: 3 http://deb.debian.org/debian trixie/main armhf python3.12-minimal armhf 3.12.8-3 [1794 kB]
Get: 4 http://deb.debian.org/debian trixie/main armhf python3-minimal armhf 3.12.8-1 [26.9 kB]
Get: 5 http://deb.debian.org/debian trixie/main armhf media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian trixie/main armhf netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian trixie/main armhf tzdata all 2024b-4 [256 kB]
Get: 8 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB]
Get: 9 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.2~rc1-2 [22.9 kB]
Get: 10 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB]
Get: 11 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B]
Get: 12 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB]
Get: 13 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB]
Get: 14 http://deb.debian.org/debian trixie/main armhf libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 15 http://deb.debian.org/debian trixie/main armhf libtirpc3t64 armhf 1.3.4+ds-1.3+b1 [71.3 kB]
Get: 16 http://deb.debian.org/debian trixie/main armhf libnsl2 armhf 1.3.0-3+b3 [35.0 kB]
Get: 17 http://deb.debian.org/debian trixie/main armhf readline-common all 8.2-6 [69.4 kB]
Get: 18 http://deb.debian.org/debian trixie/main armhf libreadline8t64 armhf 8.2-6 [146 kB]
Get: 19 http://deb.debian.org/debian trixie/main armhf libpython3.12-stdlib armhf 3.12.8-3 [1824 kB]
Get: 20 http://deb.debian.org/debian trixie/main armhf python3.12 armhf 3.12.8-3 [677 kB]
Get: 21 http://deb.debian.org/debian trixie/main armhf libpython3-stdlib armhf 3.12.8-1 [9792 B]
Get: 22 http://deb.debian.org/debian trixie/main armhf python3 armhf 3.12.8-1 [27.9 kB]
Get: 23 http://deb.debian.org/debian trixie/main armhf libpython3.13-minimal armhf 3.13.1-2 [844 kB]
Get: 24 http://deb.debian.org/debian trixie/main armhf python3.13-minimal armhf 3.13.1-2 [1838 kB]
Get: 25 http://deb.debian.org/debian trixie/main armhf sgml-base all 1.31 [15.4 kB]
Get: 26 http://deb.debian.org/debian trixie/main armhf libproc2-0 armhf 2:4.0.4-6 [56.0 kB]
Get: 27 http://deb.debian.org/debian trixie/main armhf procps armhf 2:4.0.4-6 [864 kB]
Get: 28 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB]
Get: 29 http://deb.debian.org/debian trixie/main armhf openssl armhf 3.3.2-2 [1348 kB]
Get: 30 http://deb.debian.org/debian trixie/main armhf ca-certificates all 20240203 [158 kB]
Get: 31 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB]
Get: 32 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB]
Get: 33 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB]
Get: 34 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-3 [195 kB]
Get: 35 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB]
Get: 36 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-6 [1091 kB]
Get: 37 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.2-12 [83.9 kB]
Get: 38 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB]
Get: 39 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB]
Get: 40 http://deb.debian.org/debian trixie/main armhf ucf all 3.0046 [41.1 kB]
Get: 41 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-4 [264 kB]
Get: 42 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB]
Get: 43 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 44 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 45 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-3 [723 kB]
Get: 46 http://deb.debian.org/debian trixie/main armhf bedtools armhf 2.31.1+dfsg-2 [578 kB]
Get: 47 http://deb.debian.org/debian trixie/main armhf libtcl8.6 armhf 8.6.15+dfsg-2 [934 kB]
Get: 48 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB]
Get: 49 http://deb.debian.org/debian trixie/main armhf libpng16-16t64 armhf 1.6.44-3 [263 kB]
Get: 50 http://deb.debian.org/debian trixie/main armhf libfreetype6 armhf 2.13.3+dfsg-1 [385 kB]
Get: 51 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 52 http://deb.debian.org/debian trixie/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get: 53 http://deb.debian.org/debian trixie/main armhf fontconfig-config armhf 2.15.0-1.1+b1 [318 kB]
Get: 54 http://deb.debian.org/debian trixie/main armhf libfontconfig1 armhf 2.15.0-1.1+b1 [371 kB]
Get: 55 http://deb.debian.org/debian trixie/main armhf libxau6 armhf 1:1.0.11-1 [19.7 kB]
Get: 56 http://deb.debian.org/debian trixie/main armhf libxdmcp6 armhf 1:1.1.5-1 [26.4 kB]
Get: 57 http://deb.debian.org/debian trixie/main armhf libxcb1 armhf 1.17.0-2+b1 [140 kB]
Get: 58 http://deb.debian.org/debian trixie/main armhf libx11-data all 2:1.8.10-2 [337 kB]
Get: 59 http://deb.debian.org/debian trixie/main armhf libx11-6 armhf 2:1.8.10-2 [750 kB]
Get: 60 http://deb.debian.org/debian trixie/main armhf libxrender1 armhf 1:0.9.10-1.1+b3 [25.0 kB]
Get: 61 http://deb.debian.org/debian trixie/main armhf libxft2 armhf 2.3.6-1+b3 [46.5 kB]
Get: 62 http://deb.debian.org/debian trixie/main armhf libxext6 armhf 2:1.3.4-1+b2 [45.2 kB]
Get: 63 http://deb.debian.org/debian trixie/main armhf x11-common all 1:7.7+23.1 [216 kB]
Get: 64 http://deb.debian.org/debian trixie/main armhf libxss1 armhf 1:1.2.3-1+b2 [16.4 kB]
Get: 65 http://deb.debian.org/debian trixie/main armhf libtk8.6 armhf 8.6.15-1 [697 kB]
Get: 66 http://deb.debian.org/debian trixie/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-7 [481 kB]
Get: 67 http://deb.debian.org/debian trixie/main armhf blt armhf 2.5.3+dfsg-7 [6024 B]
Get: 68 http://deb.debian.org/debian trixie/main armhf cython3 armhf 3.0.11+dfsg-1+b1 [2812 kB]
Get: 69 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.20 [89.7 kB]
Get: 70 http://deb.debian.org/debian trixie/main armhf libtool all 2.4.7-8 [517 kB]
Get: 71 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 72 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 73 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 74 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 75 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB]
Get: 76 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB]
Get: 77 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-5+b1 [9088 kB]
Get: 78 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB]
Get: 79 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-3 [1488 kB]
Get: 80 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 81 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 82 http://deb.debian.org/debian trixie/main armhf debhelper all 13.20 [915 kB]
Get: 83 http://deb.debian.org/debian trixie/main armhf python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 84 http://deb.debian.org/debian trixie/main armhf python3-more-itertools all 10.5.0-1 [63.8 kB]
Get: 85 http://deb.debian.org/debian trixie/main armhf python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 86 http://deb.debian.org/debian trixie/main armhf python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 87 http://deb.debian.org/debian trixie/main armhf python3-inflect all 7.3.1-2 [32.4 kB]
Get: 88 http://deb.debian.org/debian trixie/main armhf python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 89 http://deb.debian.org/debian trixie/main armhf python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 90 http://deb.debian.org/debian trixie/main armhf python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 91 http://deb.debian.org/debian trixie/main armhf python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 92 http://deb.debian.org/debian trixie/main armhf python3-zipp all 3.21.0-1 [10.6 kB]
Get: 93 http://deb.debian.org/debian trixie/main armhf python3-setuptools all 75.6.0-1 [720 kB]
Get: 94 http://deb.debian.org/debian trixie/main armhf dh-python all 6.20241217 [113 kB]
Get: 95 http://deb.debian.org/debian trixie/main armhf xml-core all 0.19 [20.1 kB]
Get: 96 http://deb.debian.org/debian trixie/main armhf docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 97 http://deb.debian.org/debian trixie/main armhf fontconfig armhf 2.15.0-1.1+b1 [461 kB]
Get: 98 http://deb.debian.org/debian trixie/main armhf fonts-lyx all 2.4.2.1-1 [190 kB]
Get: 99 http://deb.debian.org/debian trixie/main armhf libblas3 armhf 3.12.0-4 [111 kB]
Get: 100 http://deb.debian.org/debian trixie/main armhf libpixman-1-0 armhf 0.44.0-3 [164 kB]
Get: 101 http://deb.debian.org/debian trixie/main armhf libxcb-render0 armhf 1.17.0-2+b1 [114 kB]
Get: 102 http://deb.debian.org/debian trixie/main armhf libxcb-shm0 armhf 1.17.0-2+b1 [105 kB]
Get: 103 http://deb.debian.org/debian trixie/main armhf libcairo2 armhf 1.18.2-2 [443 kB]
Get: 104 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB]
Get: 105 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB]
Get: 106 http://deb.debian.org/debian trixie/main armhf libldap-2.5-0 armhf 2.5.19+dfsg-1 [163 kB]
Get: 107 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB]
Get: 108 http://deb.debian.org/debian trixie/main armhf libnghttp3-9 armhf 1.6.0-2 [56.8 kB]
Get: 109 http://deb.debian.org/debian trixie/main armhf libngtcp2-16 armhf 1.9.1-1 [115 kB]
Get: 110 http://deb.debian.org/debian trixie/main armhf libngtcp2-crypto-gnutls8 armhf 1.9.1-1 [15.8 kB]
Get: 111 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB]
Get: 112 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB]
Get: 113 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB]
Get: 114 http://deb.debian.org/debian trixie/main armhf libcurl3t64-gnutls armhf 8.11.1-1 [311 kB]
Get: 115 http://deb.debian.org/debian trixie/main armhf libcurl4t64 armhf 8.11.1-1 [303 kB]
Get: 116 http://deb.debian.org/debian trixie/main armhf libdatrie1 armhf 0.2.13-3+b1 [34.7 kB]
Get: 117 http://deb.debian.org/debian trixie/main armhf libdeflate0 armhf 1.22-1 [36.3 kB]
Get: 118 http://deb.debian.org/debian trixie/main armhf libexpat1-dev armhf 2.6.4-1 [140 kB]
Get: 119 http://deb.debian.org/debian trixie/main armhf libfribidi0 armhf 1.0.16-1 [24.6 kB]
Get: 120 http://deb.debian.org/debian trixie/main armhf libgfortran5 armhf 14.2.0-8 [263 kB]
Get: 121 http://deb.debian.org/debian trixie/main armhf libglib2.0-0t64 armhf 2.82.4-1 [1327 kB]
Get: 122 http://deb.debian.org/debian trixie/main armhf libgraphite2-3 armhf 1.3.14-2+b1 [63.1 kB]
Get: 123 http://deb.debian.org/debian trixie/main armhf libharfbuzz0b armhf 10.1.0-1 [418 kB]
Get: 124 http://deb.debian.org/debian trixie/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB]
Get: 125 http://deb.debian.org/debian trixie/main armhf libhts3t64 armhf 1.20+ds-2 [401 kB]
Get: 126 http://deb.debian.org/debian trixie/main armhf libice6 armhf 2:1.1.1-1 [58.5 kB]
Get: 127 http://deb.debian.org/debian trixie/main armhf libimagequant0 armhf 2.18.0-1+b2 [30.5 kB]
Get: 128 http://deb.debian.org/debian trixie/main armhf libjbig0 armhf 2.1-6.1+b2 [27.3 kB]
Get: 129 http://deb.debian.org/debian trixie/main armhf libjpeg62-turbo armhf 1:2.1.5-3+b1 [145 kB]
Get: 130 http://deb.debian.org/debian trixie/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 131 http://deb.debian.org/debian trixie/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 132 http://deb.debian.org/debian trixie/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 133 http://deb.debian.org/debian trixie/main armhf libjs-sphinxdoc all 8.1.3-3 [30.4 kB]
Get: 134 http://deb.debian.org/debian trixie/main armhf libjson-perl all 4.10000-1 [87.5 kB]
Get: 135 http://deb.debian.org/debian trixie/main armhf liblapack3 armhf 3.12.0-4 [1828 kB]
Get: 136 http://deb.debian.org/debian trixie/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1+b2 [25.6 kB]
Get: 137 http://deb.debian.org/debian trixie/main armhf liblcms2-2 armhf 2.16-2 [131 kB]
Get: 138 http://deb.debian.org/debian trixie/main armhf liblerc4 armhf 4.0.0+ds-5 [146 kB]
Get: 139 http://deb.debian.org/debian trixie/main armhf libopenjp2-7 armhf 2.5.0-2+b4 [179 kB]
Get: 140 http://deb.debian.org/debian trixie/main armhf libthai-data all 0.1.29-2 [168 kB]
Get: 141 http://deb.debian.org/debian trixie/main armhf libthai0 armhf 0.1.29-2+b1 [46.0 kB]
Get: 142 http://deb.debian.org/debian trixie/main armhf libpango-1.0-0 armhf 1.55.0+ds-3 [200 kB]
Get: 143 http://deb.debian.org/debian trixie/main armhf libpangoft2-1.0-0 armhf 1.55.0+ds-3 [47.7 kB]
Get: 144 http://deb.debian.org/debian trixie/main armhf libpangocairo-1.0-0 armhf 1.55.0+ds-3 [31.3 kB]
Get: 145 http://deb.debian.org/debian trixie/main armhf libpaper2 armhf 2.2.5-0.3 [15.6 kB]
Get: 146 http://deb.debian.org/debian trixie/main armhf libpaper-utils armhf 2.2.5-0.3 [14.9 kB]
Get: 147 http://deb.debian.org/debian trixie/main armhf libpython3.12t64 armhf 3.12.8-3 [1849 kB]
Get: 148 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB]
Get: 149 http://deb.debian.org/debian trixie/main armhf libpython3.12-dev armhf 3.12.8-3 [3812 kB]
Get: 150 http://deb.debian.org/debian trixie/main armhf libpython3-dev armhf 3.12.8-1 [10.1 kB]
Get: 151 http://deb.debian.org/debian trixie/main armhf libpython3.13-stdlib armhf 3.13.1-2 [1846 kB]
Get: 152 http://deb.debian.org/debian trixie/main armhf libpython3.13 armhf 3.13.1-2 [1870 kB]
Get: 153 http://deb.debian.org/debian trixie/main armhf libpython3.13-dev armhf 3.13.1-2 [3801 kB]
Get: 154 http://deb.debian.org/debian trixie/main armhf libpython3-all-dev armhf 3.12.8-1 [1068 B]
Get: 155 http://deb.debian.org/debian trixie/main armhf libqhull-r8.0 armhf 2020.2-6+b2 [220 kB]
Get: 156 http://deb.debian.org/debian trixie/main armhf libraqm0 armhf 0.10.2-1 [11.6 kB]
Get: 157 http://deb.debian.org/debian trixie/main armhf libsharpyuv0 armhf 1.4.0-0.1+b1 [111 kB]
Get: 158 http://deb.debian.org/debian trixie/main armhf libsm6 armhf 2:1.2.4-1 [33.5 kB]
Get: 159 http://deb.debian.org/debian trixie/main armhf libwebp7 armhf 1.4.0-0.1+b1 [266 kB]
Get: 160 http://deb.debian.org/debian trixie/main armhf libtiff6 armhf 4.5.1+git230720-5 [302 kB]
Get: 161 http://deb.debian.org/debian trixie/main armhf libwebpdemux2 armhf 1.4.0-0.1+b1 [110 kB]
Get: 162 http://deb.debian.org/debian trixie/main armhf libwebpmux3 armhf 1.4.0-0.1+b1 [120 kB]
Get: 163 http://deb.debian.org/debian trixie/main armhf libxslt1.1 armhf 1.1.35-1.1+b1 [212 kB]
Get: 164 http://deb.debian.org/debian trixie/main armhf libxt6t64 armhf 1:1.2.1-1.2+b1 [160 kB]
Get: 165 http://deb.debian.org/debian trixie/main armhf libyaml-0-2 armhf 0.2.5-2 [45.4 kB]
Get: 166 http://deb.debian.org/debian trixie/main armhf python3-packaging all 24.2-1 [55.3 kB]
Get: 167 http://deb.debian.org/debian trixie/main armhf python3-pyproject-hooks all 1.2.0-1 [11.7 kB]
Get: 168 http://deb.debian.org/debian trixie/main armhf python3-toml all 0.10.2-1 [16.2 kB]
Get: 169 http://deb.debian.org/debian trixie/main armhf python3-wheel all 0.45.1-1 [56.7 kB]
Get: 170 http://deb.debian.org/debian trixie/main armhf python3-build all 1.2.2-1 [36.0 kB]
Get: 171 http://deb.debian.org/debian trixie/main armhf python3-installer all 0.7.0+dfsg1-3 [18.6 kB]
Get: 172 http://deb.debian.org/debian trixie/main armhf pybuild-plugin-pyproject all 6.20241217 [11.5 kB]
Get: 173 http://deb.debian.org/debian trixie/main armhf python-babel-localedata all 2.16.0-1 [5696 kB]
Get: 174 http://deb.debian.org/debian trixie/main armhf python-matplotlib-data all 3.8.3-3 [2731 kB]
Get: 175 http://deb.debian.org/debian trixie/main armhf python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 176 http://deb.debian.org/debian trixie/main armhf python3.13 armhf 3.13.1-2 [740 kB]
Get: 177 http://deb.debian.org/debian trixie/main armhf python3-all armhf 3.12.8-1 [1048 B]
Get: 178 http://deb.debian.org/debian trixie/main armhf python3.12-dev armhf 3.12.8-3 [506 kB]
Get: 179 http://deb.debian.org/debian trixie/main armhf python3-dev armhf 3.12.8-1 [26.1 kB]
Get: 180 http://deb.debian.org/debian trixie/main armhf python3.13-dev armhf 3.13.1-2 [505 kB]
Get: 181 http://deb.debian.org/debian trixie/main armhf python3-all-dev armhf 3.12.8-1 [1068 B]
Get: 182 http://deb.debian.org/debian trixie/main armhf python3-attr all 24.2.0-1 [68.4 kB]
Get: 183 http://deb.debian.org/debian trixie/main armhf python3-babel all 2.16.0-1 [114 kB]
Get: 184 http://deb.debian.org/debian trixie/main armhf python3-brotli armhf 1.1.0-2+b6 [302 kB]
Get: 185 http://deb.debian.org/debian trixie/main armhf python3-certifi all 2024.8.30+dfsg-1 [9576 B]
Get: 186 http://deb.debian.org/debian trixie/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get: 187 http://deb.debian.org/debian trixie/main armhf python3-charset-normalizer armhf 3.4.0-1+b1 [126 kB]
Get: 188 http://deb.debian.org/debian trixie/main armhf python3-numpy armhf 1:1.26.4+ds-12 [3676 kB]
Get: 189 http://deb.debian.org/debian trixie/main armhf python3-contourpy armhf 1.3.1-1 [217 kB]
Get: 190 http://deb.debian.org/debian trixie/main armhf python3-cycler all 0.12.1-1 [9496 B]
Get: 191 http://deb.debian.org/debian trixie/main armhf python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 192 http://deb.debian.org/debian trixie/main armhf python3-decorator all 5.1.1-5 [15.1 kB]
Get: 193 http://deb.debian.org/debian trixie/main armhf python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 194 http://deb.debian.org/debian trixie/main armhf python3-roman all 4.2-1 [10.4 kB]
Get: 195 http://deb.debian.org/debian trixie/main armhf python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 196 http://deb.debian.org/debian trixie/main armhf python3-tz all 2024.2-1 [31.0 kB]
Get: 197 http://deb.debian.org/debian trixie/main armhf python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 198 http://deb.debian.org/debian trixie/main armhf python3-fs all 2.4.16-5.1 [95.2 kB]
Get: 199 http://deb.debian.org/debian trixie/main armhf python3-lxml armhf 5.3.0-1+b1 [1468 kB]
Get: 200 http://deb.debian.org/debian trixie/main armhf python3-lz4 armhf 4.4.0+dfsg-1 [23.9 kB]
Get: 201 http://deb.debian.org/debian trixie/main armhf python3-scipy armhf 1.14.1-3 [17.8 MB]
Get: 202 http://deb.debian.org/debian trixie/main armhf python3-mpmath all 1.3.0-1 [419 kB]
Get: 203 http://deb.debian.org/debian trixie/main armhf python3-sympy all 1.13.3-1 [4147 kB]
Get: 204 http://deb.debian.org/debian trixie/main armhf python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get: 205 http://deb.debian.org/debian trixie/main armhf unicode-data all 15.1.0-1 [8547 kB]
Get: 206 http://deb.debian.org/debian trixie/main armhf python3-fonttools armhf 4.55.0-3 [1529 kB]
Get: 207 http://deb.debian.org/debian trixie/main armhf python3-idna all 3.8-2 [41.6 kB]
Get: 208 http://deb.debian.org/debian trixie/main armhf python3-imagesize all 1.4.1-1 [6688 B]
Get: 209 http://deb.debian.org/debian trixie/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get: 210 http://deb.debian.org/debian trixie/main armhf python3-markupsafe armhf 2.1.5-1+b2 [13.4 kB]
Get: 211 http://deb.debian.org/debian trixie/main armhf python3-jinja2 all 3.1.3-1.1 [120 kB]
Get: 212 http://deb.debian.org/debian trixie/main armhf python3-kiwisolver armhf 1.4.7-2+b1 [64.9 kB]
Get: 213 http://deb.debian.org/debian trixie/main armhf python3-pil armhf 10.4.0-1+b1 [478 kB]
Get: 214 http://deb.debian.org/debian trixie/main armhf python3.12-tk armhf 3.12.8-3 [109 kB]
Get: 215 http://deb.debian.org/debian trixie/main armhf python3.13-tk armhf 3.13.1-2 [99.7 kB]
Get: 216 http://deb.debian.org/debian trixie/main armhf python3-tk armhf 3.13.1-1 [9464 B]
Get: 217 http://deb.debian.org/debian trixie/main armhf python3-pil.imagetk armhf 10.4.0-1+b1 [79.3 kB]
Get: 218 http://deb.debian.org/debian trixie/main armhf python3-pyparsing all 3.1.2-1 [146 kB]
Get: 219 http://deb.debian.org/debian trixie/main armhf python3-matplotlib armhf 3.8.3-3+b1 [5579 kB]
Get: 220 http://deb.debian.org/debian trixie/main armhf sphinx-common all 8.1.3-3 [617 kB]
Get: 221 http://deb.debian.org/debian trixie/main armhf python3-pygments all 2.18.0+dfsg-1 [836 kB]
Get: 222 http://deb.debian.org/debian trixie/main armhf python3-urllib3 all 2.2.3-4 [112 kB]
Get: 223 http://deb.debian.org/debian trixie/main armhf python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 224 http://deb.debian.org/debian trixie/main armhf python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 225 http://deb.debian.org/debian trixie/main armhf python3-sphinx all 8.1.3-3 [468 kB]
Get: 226 http://deb.debian.org/debian trixie/main armhf python3-tabulate all 0.9.0-1 [45.9 kB]
Get: 227 http://deb.debian.org/debian trixie/main armhf python3-numpydoc all 1.8.0-1 [51.4 kB]
Get: 228 http://deb.debian.org/debian trixie/main armhf python3-pandas-lib armhf 2.2.3+dfsg-5+b1 [6440 kB]
Get: 229 http://deb.debian.org/debian trixie/main armhf python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get: 230 http://deb.debian.org/debian trixie/main armhf python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 231 http://deb.debian.org/debian trixie/main armhf python3-psutil armhf 5.9.8-2 [225 kB]
Get: 232 http://deb.debian.org/debian trixie/main armhf python3-pysam armhf 0.22.1+ds-2+b2 [3755 kB]
Get: 233 http://deb.debian.org/debian trixie/main armhf python3-pytest all 8.3.3-1 [249 kB]
Get: 234 http://deb.debian.org/debian trixie/main armhf python3-yaml armhf 6.0.2-1+b1 [158 kB]
Get: 235 http://deb.debian.org/debian trixie/main armhf zip armhf 3.0-14 [221 kB]
Get: 236 http://deb.debian.org/debian trixie/main armhf unzip armhf 6.0-28 [152 kB]
Get: 237 http://deb.debian.org/debian trixie/main armhf xdg-utils all 1.2.1-2 [75.8 kB]
Get: 238 http://deb.debian.org/debian trixie/main armhf r-base-core armhf 4.4.2-1 [28.0 MB]
Fetched 169 MB in 11s (14.9 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.12-minimal:armhf.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19680 files and directories currently installed.)
Preparing to unpack .../libpython3.12-minimal_3.12.8-3_armhf.deb ...
Unpacking libpython3.12-minimal:armhf (3.12.8-3) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../libexpat1_2.6.4-1_armhf.deb ...
Unpacking libexpat1:armhf (2.6.4-1) ...
Selecting previously unselected package python3.12-minimal.
Preparing to unpack .../python3.12-minimal_3.12.8-3_armhf.deb ...
Unpacking python3.12-minimal (3.12.8-3) ...
Setting up libpython3.12-minimal:armhf (3.12.8-3) ...
Setting up libexpat1:armhf (2.6.4-1) ...
Setting up python3.12-minimal (3.12.8-3) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 20000 files and directories currently installed.)
Preparing to unpack .../00-python3-minimal_3.12.8-1_armhf.deb ...
Unpacking python3-minimal (3.12.8-1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../01-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../02-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../03-tzdata_2024b-4_all.deb ...
Unpacking tzdata (2024b-4) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../04-libkrb5support0_1.21.3-3_armhf.deb ...
Unpacking libkrb5support0:armhf (1.21.3-3) ...
Selecting previously unselected package libcom-err2:armhf.
Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_armhf.deb ...
Unpacking libcom-err2:armhf (1.47.2~rc1-2) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../06-libk5crypto3_1.21.3-3_armhf.deb ...
Unpacking libk5crypto3:armhf (1.21.3-3) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../07-libkeyutils1_1.6.3-4_armhf.deb ...
Unpacking libkeyutils1:armhf (1.6.3-4) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../08-libkrb5-3_1.21.3-3_armhf.deb ...
Unpacking libkrb5-3:armhf (1.21.3-3) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.21.3-3) ...
Selecting previously unselected package libtirpc-common.
Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ...
Unpacking libtirpc-common (1.3.4+ds-1.3) ...
Selecting previously unselected package libtirpc3t64:armhf.
Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_armhf.deb ...
Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3 to /lib/arm-linux-gnueabihf/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0 to /lib/arm-linux-gnueabihf/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ...
Selecting previously unselected package libnsl2:armhf.
Preparing to unpack .../12-libnsl2_1.3.0-3+b3_armhf.deb ...
Unpacking libnsl2:armhf (1.3.0-3+b3) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../13-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:armhf.
Preparing to unpack .../14-libreadline8t64_8.2-6_armhf.deb ...
Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8 to /lib/arm-linux-gnueabihf/libhistory.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libhistory.so.8.2 to /lib/arm-linux-gnueabihf/libhistory.so.8.2.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8 to /lib/arm-linux-gnueabihf/libreadline.so.8.usr-is-merged by libreadline8t64'
Adding 'diversion of /lib/arm-linux-gnueabihf/libreadline.so.8.2 to /lib/arm-linux-gnueabihf/libreadline.so.8.2.usr-is-merged by libreadline8t64'
Unpacking libreadline8t64:armhf (8.2-6) ...
Selecting previously unselected package libpython3.12-stdlib:armhf.
Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_armhf.deb ...
Unpacking libpython3.12-stdlib:armhf (3.12.8-3) ...
Selecting previously unselected package python3.12.
Preparing to unpack .../16-python3.12_3.12.8-3_armhf.deb ...
Unpacking python3.12 (3.12.8-3) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../17-libpython3-stdlib_3.12.8-1_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.12.8-1) ...
Setting up python3-minimal (3.12.8-1) ...
Selecting previously unselected package python3.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 21063 files and directories currently installed.)
Preparing to unpack .../000-python3_3.12.8-1_armhf.deb ...
Unpacking python3 (3.12.8-1) ...
Selecting previously unselected package libpython3.13-minimal:armhf.
Preparing to unpack .../001-libpython3.13-minimal_3.13.1-2_armhf.deb ...
Unpacking libpython3.13-minimal:armhf (3.13.1-2) ...
Selecting previously unselected package python3.13-minimal.
Preparing to unpack .../002-python3.13-minimal_3.13.1-2_armhf.deb ...
Unpacking python3.13-minimal (3.13.1-2) ...
Selecting previously unselected package sgml-base.
Preparing to unpack .../003-sgml-base_1.31_all.deb ...
Unpacking sgml-base (1.31) ...
Selecting previously unselected package libproc2-0:armhf.
Preparing to unpack .../004-libproc2-0_2%3a4.0.4-6_armhf.deb ...
Unpacking libproc2-0:armhf (2:4.0.4-6) ...
Selecting previously unselected package procps.
Preparing to unpack .../005-procps_2%3a4.0.4-6_armhf.deb ...
Unpacking procps (2:4.0.4-6) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../006-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package openssl.
Preparing to unpack .../007-openssl_3.3.2-2_armhf.deb ...
Unpacking openssl (3.3.2-2) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../008-ca-certificates_20240203_all.deb ...
Unpacking ca-certificates (20240203) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../009-libmagic-mgc_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:armhf.
Preparing to unpack .../010-libmagic1t64_1%3a5.45-3+b1_armhf.deb ...
Unpacking libmagic1t64:armhf (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../011-file_1%3a5.45-3+b1_armhf.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../012-gettext-base_0.22.5-3_armhf.deb ...
Unpacking gettext-base (0.22.5-3) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../013-libuchardet0_0.0.8-1+b2_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../014-groff-base_1.23.0-6_armhf.deb ...
Unpacking groff-base (1.23.0-6) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../015-bsdextrautils_2.40.2-12_armhf.deb ...
Unpacking bsdextrautils (2.40.2-12) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../016-libpipeline1_1.5.8-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../017-man-db_2.13.0-1_armhf.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package ucf.
Preparing to unpack .../018-ucf_3.0046_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0046) ...
Selecting previously unselected package m4.
Preparing to unpack .../019-m4_1.4.19-4_armhf.deb ...
Unpacking m4 (1.4.19-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../020-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../021-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../022-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../023-autopoint_0.22.5-3_all.deb ...
Unpacking autopoint (0.22.5-3) ...
Selecting previously unselected package bedtools.
Preparing to unpack .../024-bedtools_2.31.1+dfsg-2_armhf.deb ...
Unpacking bedtools (2.31.1+dfsg-2) ...
Selecting previously unselected package libtcl8.6:armhf.
Preparing to unpack .../025-libtcl8.6_8.6.15+dfsg-2_armhf.deb ...
Unpacking libtcl8.6:armhf (8.6.15+dfsg-2) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../026-libbrotli1_1.1.0-2+b6_armhf.deb ...
Unpacking libbrotli1:armhf (1.1.0-2+b6) ...
Selecting previously unselected package libpng16-16t64:armhf.
Preparing to unpack .../027-libpng16-16t64_1.6.44-3_armhf.deb ...
Unpacking libpng16-16t64:armhf (1.6.44-3) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../028-libfreetype6_2.13.3+dfsg-1_armhf.deb ...
Unpacking libfreetype6:armhf (2.13.3+dfsg-1) ...
Selecting previously unselected package fonts-dejavu-mono.
Preparing to unpack .../029-fonts-dejavu-mono_2.37-8_all.deb ...
Unpacking fonts-dejavu-mono (2.37-8) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../030-fonts-dejavu-core_2.37-8_all.deb ...
Unpacking fonts-dejavu-core (2.37-8) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../031-fontconfig-config_2.15.0-1.1+b1_armhf.deb ...
Unpacking fontconfig-config (2.15.0-1.1+b1) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../032-libfontconfig1_2.15.0-1.1+b1_armhf.deb ...
Unpacking libfontconfig1:armhf (2.15.0-1.1+b1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../033-libxau6_1%3a1.0.11-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.11-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../034-libxdmcp6_1%3a1.1.5-1_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.5-1) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../035-libxcb1_1.17.0-2+b1_armhf.deb ...
Unpacking libxcb1:armhf (1.17.0-2+b1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../036-libx11-data_2%3a1.8.10-2_all.deb ...
Unpacking libx11-data (2:1.8.10-2) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../037-libx11-6_2%3a1.8.10-2_armhf.deb ...
Unpacking libx11-6:armhf (2:1.8.10-2) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../038-libxrender1_1%3a0.9.10-1.1+b3_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1.1+b3) ...
Selecting previously unselected package libxft2:armhf.
Preparing to unpack .../039-libxft2_2.3.6-1+b3_armhf.deb ...
Unpacking libxft2:armhf (2.3.6-1+b3) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../040-libxext6_2%3a1.3.4-1+b2_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.4-1+b2) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../041-x11-common_1%3a7.7+23.1_all.deb ...
Unpacking x11-common (1:7.7+23.1) ...
Selecting previously unselected package libxss1:armhf.
Preparing to unpack .../042-libxss1_1%3a1.2.3-1+b2_armhf.deb ...
Unpacking libxss1:armhf (1:1.2.3-1+b2) ...
Selecting previously unselected package libtk8.6:armhf.
Preparing to unpack .../043-libtk8.6_8.6.15-1_armhf.deb ...
Unpacking libtk8.6:armhf (8.6.15-1) ...
Selecting previously unselected package tk8.6-blt2.5.
Preparing to unpack .../044-tk8.6-blt2.5_2.5.3+dfsg-7_armhf.deb ...
Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ...
Selecting previously unselected package blt.
Preparing to unpack .../045-blt_2.5.3+dfsg-7_armhf.deb ...
Unpacking blt (2.5.3+dfsg-7) ...
Selecting previously unselected package cython3.
Preparing to unpack .../046-cython3_3.0.11+dfsg-1+b1_armhf.deb ...
Unpacking cython3 (3.0.11+dfsg-1+b1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../047-libdebhelper-perl_13.20_all.deb ...
Unpacking libdebhelper-perl (13.20) ...
Selecting previously unselected package libtool.
Preparing to unpack .../048-libtool_2.4.7-8_all.deb ...
Unpacking libtool (2.4.7-8) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../049-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../050-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../051-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../052-dh-strip-nondeterminism_1.14.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.0-1) ...
Selecting previously unselected package libelf1t64:armhf.
Preparing to unpack .../053-libelf1t64_0.192-4_armhf.deb ...
Unpacking libelf1t64:armhf (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../054-dwz_0.15-1+b2_armhf.deb ...
Unpacking dwz (0.15-1+b2) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../055-libicu72_72.1-5+b1_armhf.deb ...
Unpacking libicu72:armhf (72.1-5+b1) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../056-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ...
Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../057-gettext_0.22.5-3_armhf.deb ...
Unpacking gettext (0.22.5-3) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../058-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../059-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../060-debhelper_13.20_all.deb ...
Unpacking debhelper (13.20) ...
Selecting previously unselected package python3-autocommand.
Preparing to unpack .../061-python3-autocommand_2.2.2-3_all.deb ...
Unpacking python3-autocommand (2.2.2-3) ...
Selecting previously unselected package python3-more-itertools.
Preparing to unpack .../062-python3-more-itertools_10.5.0-1_all.deb ...
Unpacking python3-more-itertools (10.5.0-1) ...
Selecting previously unselected package python3-typing-extensions.
Preparing to unpack .../063-python3-typing-extensions_4.12.2-2_all.deb ...
Unpacking python3-typing-extensions (4.12.2-2) ...
Selecting previously unselected package python3-typeguard.
Preparing to unpack .../064-python3-typeguard_4.4.1-1_all.deb ...
Unpacking python3-typeguard (4.4.1-1) ...
Selecting previously unselected package python3-inflect.
Preparing to unpack .../065-python3-inflect_7.3.1-2_all.deb ...
Unpacking python3-inflect (7.3.1-2) ...
Selecting previously unselected package python3-jaraco.context.
Preparing to unpack .../066-python3-jaraco.context_6.0.0-1_all.deb ...
Unpacking python3-jaraco.context (6.0.0-1) ...
Selecting previously unselected package python3-jaraco.functools.
Preparing to unpack .../067-python3-jaraco.functools_4.1.0-1_all.deb ...
Unpacking python3-jaraco.functools (4.1.0-1) ...
Selecting previously unselected package python3-pkg-resources.
Preparing to unpack .../068-python3-pkg-resources_75.6.0-1_all.deb ...
Unpacking python3-pkg-resources (75.6.0-1) ...
Selecting previously unselected package python3-jaraco.text.
Preparing to unpack .../069-python3-jaraco.text_4.0.0-1_all.deb ...
Unpacking python3-jaraco.text (4.0.0-1) ...
Selecting previously unselected package python3-zipp.
Preparing to unpack .../070-python3-zipp_3.21.0-1_all.deb ...
Unpacking python3-zipp (3.21.0-1) ...
Selecting previously unselected package python3-setuptools.
Preparing to unpack .../071-python3-setuptools_75.6.0-1_all.deb ...
Unpacking python3-setuptools (75.6.0-1) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../072-dh-python_6.20241217_all.deb ...
Unpacking dh-python (6.20241217) ...
Selecting previously unselected package xml-core.
Preparing to unpack .../073-xml-core_0.19_all.deb ...
Unpacking xml-core (0.19) ...
Selecting previously unselected package docutils-common.
Preparing to unpack .../074-docutils-common_0.21.2+dfsg-2_all.deb ...
Unpacking docutils-common (0.21.2+dfsg-2) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../075-fontconfig_2.15.0-1.1+b1_armhf.deb ...
Unpacking fontconfig (2.15.0-1.1+b1) ...
Selecting previously unselected package fonts-lyx.
Preparing to unpack .../076-fonts-lyx_2.4.2.1-1_all.deb ...
Unpacking fonts-lyx (2.4.2.1-1) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../077-libblas3_3.12.0-4_armhf.deb ...
Unpacking libblas3:armhf (3.12.0-4) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../078-libpixman-1-0_0.44.0-3_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.44.0-3) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../079-libxcb-render0_1.17.0-2+b1_armhf.deb ...
Unpacking libxcb-render0:armhf (1.17.0-2+b1) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../080-libxcb-shm0_1.17.0-2+b1_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.17.0-2+b1) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../081-libcairo2_1.18.2-2_armhf.deb ...
Unpacking libcairo2:armhf (1.18.2-2) ...
Selecting previously unselected package libsasl2-modules-db:armhf.
Preparing to unpack .../082-libsasl2-modules-db_2.1.28+dfsg1-8_armhf.deb ...
Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ...
Selecting previously unselected package libsasl2-2:armhf.
Preparing to unpack .../083-libsasl2-2_2.1.28+dfsg1-8_armhf.deb ...
Unpacking libsasl2-2:armhf (2.1.28+dfsg1-8) ...
Selecting previously unselected package libldap-2.5-0:armhf.
Preparing to unpack .../084-libldap-2.5-0_2.5.19+dfsg-1_armhf.deb ...
Unpacking libldap-2.5-0:armhf (2.5.19+dfsg-1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../085-libnghttp2-14_1.64.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.64.0-1) ...
Selecting previously unselected package libnghttp3-9:armhf.
Preparing to unpack .../086-libnghttp3-9_1.6.0-2_armhf.deb ...
Unpacking libnghttp3-9:armhf (1.6.0-2) ...
Selecting previously unselected package libngtcp2-16:armhf.
Preparing to unpack .../087-libngtcp2-16_1.9.1-1_armhf.deb ...
Unpacking libngtcp2-16:armhf (1.9.1-1) ...
Selecting previously unselected package libngtcp2-crypto-gnutls8:armhf.
Preparing to unpack .../088-libngtcp2-crypto-gnutls8_1.9.1-1_armhf.deb ...
Unpacking libngtcp2-crypto-gnutls8:armhf (1.9.1-1) ...
Selecting previously unselected package libpsl5t64:armhf.
Preparing to unpack .../089-libpsl5t64_0.21.2-1.1+b1_armhf.deb ...
Unpacking libpsl5t64:armhf (0.21.2-1.1+b1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../090-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ...
Selecting previously unselected package libssh2-1t64:armhf.
Preparing to unpack .../091-libssh2-1t64_1.11.1-1_armhf.deb ...
Unpacking libssh2-1t64:armhf (1.11.1-1) ...
Selecting previously unselected package libcurl3t64-gnutls:armhf.
Preparing to unpack .../092-libcurl3t64-gnutls_8.11.1-1_armhf.deb ...
Unpacking libcurl3t64-gnutls:armhf (8.11.1-1) ...
Selecting previously unselected package libcurl4t64:armhf.
Preparing to unpack .../093-libcurl4t64_8.11.1-1_armhf.deb ...
Unpacking libcurl4t64:armhf (8.11.1-1) ...
Selecting previously unselected package libdatrie1:armhf.
Preparing to unpack .../094-libdatrie1_0.2.13-3+b1_armhf.deb ...
Unpacking libdatrie1:armhf (0.2.13-3+b1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../095-libdeflate0_1.22-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.22-1) ...
Selecting previously unselected package libexpat1-dev:armhf.
Preparing to unpack .../096-libexpat1-dev_2.6.4-1_armhf.deb ...
Unpacking libexpat1-dev:armhf (2.6.4-1) ...
Selecting previously unselected package libfribidi0:armhf.
Preparing to unpack .../097-libfribidi0_1.0.16-1_armhf.deb ...
Unpacking libfribidi0:armhf (1.0.16-1) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../098-libgfortran5_14.2.0-8_armhf.deb ...
Unpacking libgfortran5:armhf (14.2.0-8) ...
Selecting previously unselected package libglib2.0-0t64:armhf.
Preparing to unpack .../099-libglib2.0-0t64_2.82.4-1_armhf.deb ...
Unpacking libglib2.0-0t64:armhf (2.82.4-1) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../100-libgraphite2-3_1.3.14-2+b1_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.14-2+b1) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../101-libharfbuzz0b_10.1.0-1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (10.1.0-1) ...
Selecting previously unselected package libhtscodecs2:armhf.
Preparing to unpack .../102-libhtscodecs2_1.6.1-1_armhf.deb ...
Unpacking libhtscodecs2:armhf (1.6.1-1) ...
Selecting previously unselected package libhts3t64:armhf.
Preparing to unpack .../103-libhts3t64_1.20+ds-2_armhf.deb ...
Unpacking libhts3t64:armhf (1.20+ds-2) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../104-libice6_2%3a1.1.1-1_armhf.deb ...
Unpacking libice6:armhf (2:1.1.1-1) ...
Selecting previously unselected package libimagequant0:armhf.
Preparing to unpack .../105-libimagequant0_2.18.0-1+b2_armhf.deb ...
Unpacking libimagequant0:armhf (2.18.0-1+b2) ...
Selecting previously unselected package libjbig0:armhf.
Preparing to unpack .../106-libjbig0_2.1-6.1+b2_armhf.deb ...
Unpacking libjbig0:armhf (2.1-6.1+b2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../107-libjpeg62-turbo_1%3a2.1.5-3+b1_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.1.5-3+b1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../108-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../109-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
Selecting previously unselected package libjs-underscore.
Preparing to unpack .../110-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Selecting previously unselected package libjs-sphinxdoc.
Preparing to unpack .../111-libjs-sphinxdoc_8.1.3-3_all.deb ...
Unpacking libjs-sphinxdoc (8.1.3-3) ...
Selecting previously unselected package libjson-perl.
Preparing to unpack .../112-libjson-perl_4.10000-1_all.deb ...
Unpacking libjson-perl (4.10000-1) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../113-liblapack3_3.12.0-4_armhf.deb ...
Unpacking liblapack3:armhf (3.12.0-4) ...
Selecting previously unselected package liblbfgsb0:armhf.
Preparing to unpack .../114-liblbfgsb0_3.0+dfsg.4-1+b2_armhf.deb ...
Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1+b2) ...
Selecting previously unselected package liblcms2-2:armhf.
Preparing to unpack .../115-liblcms2-2_2.16-2_armhf.deb ...
Unpacking liblcms2-2:armhf (2.16-2) ...
Selecting previously unselected package liblerc4:armhf.
Preparing to unpack .../116-liblerc4_4.0.0+ds-5_armhf.deb ...
Unpacking liblerc4:armhf (4.0.0+ds-5) ...
Selecting previously unselected package libopenjp2-7:armhf.
Preparing to unpack .../117-libopenjp2-7_2.5.0-2+b4_armhf.deb ...
Unpacking libopenjp2-7:armhf (2.5.0-2+b4) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../118-libthai-data_0.1.29-2_all.deb ...
Unpacking libthai-data (0.1.29-2) ...
Selecting previously unselected package libthai0:armhf.
Preparing to unpack .../119-libthai0_0.1.29-2+b1_armhf.deb ...
Unpacking libthai0:armhf (0.1.29-2+b1) ...
Selecting previously unselected package libpango-1.0-0:armhf.
Preparing to unpack .../120-libpango-1.0-0_1.55.0+ds-3_armhf.deb ...
Unpacking libpango-1.0-0:armhf (1.55.0+ds-3) ...
Selecting previously unselected package libpangoft2-1.0-0:armhf.
Preparing to unpack .../121-libpangoft2-1.0-0_1.55.0+ds-3_armhf.deb ...
Unpacking libpangoft2-1.0-0:armhf (1.55.0+ds-3) ...
Selecting previously unselected package libpangocairo-1.0-0:armhf.
Preparing to unpack .../122-libpangocairo-1.0-0_1.55.0+ds-3_armhf.deb ...
Unpacking libpangocairo-1.0-0:armhf (1.55.0+ds-3) ...
Selecting previously unselected package libpaper2:armhf.
Preparing to unpack .../123-libpaper2_2.2.5-0.3_armhf.deb ...
Unpacking libpaper2:armhf (2.2.5-0.3) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../124-libpaper-utils_2.2.5-0.3_armhf.deb ...
Unpacking libpaper-utils (2.2.5-0.3) ...
Selecting previously unselected package libpython3.12t64:armhf.
Preparing to unpack .../125-libpython3.12t64_3.12.8-3_armhf.deb ...
Unpacking libpython3.12t64:armhf (3.12.8-3) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../126-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ...
Selecting previously unselected package libpython3.12-dev:armhf.
Preparing to unpack .../127-libpython3.12-dev_3.12.8-3_armhf.deb ...
Unpacking libpython3.12-dev:armhf (3.12.8-3) ...
Selecting previously unselected package libpython3-dev:armhf.
Preparing to unpack .../128-libpython3-dev_3.12.8-1_armhf.deb ...
Unpacking libpython3-dev:armhf (3.12.8-1) ...
Selecting previously unselected package libpython3.13-stdlib:armhf.
Preparing to unpack .../129-libpython3.13-stdlib_3.13.1-2_armhf.deb ...
Unpacking libpython3.13-stdlib:armhf (3.13.1-2) ...
Selecting previously unselected package libpython3.13:armhf.
Preparing to unpack .../130-libpython3.13_3.13.1-2_armhf.deb ...
Unpacking libpython3.13:armhf (3.13.1-2) ...
Selecting previously unselected package libpython3.13-dev:armhf.
Preparing to unpack .../131-libpython3.13-dev_3.13.1-2_armhf.deb ...
Unpacking libpython3.13-dev:armhf (3.13.1-2) ...
Selecting previously unselected package libpython3-all-dev:armhf.
Preparing to unpack .../132-libpython3-all-dev_3.12.8-1_armhf.deb ...
Unpacking libpython3-all-dev:armhf (3.12.8-1) ...
Selecting previously unselected package libqhull-r8.0:armhf.
Preparing to unpack .../133-libqhull-r8.0_2020.2-6+b2_armhf.deb ...
Unpacking libqhull-r8.0:armhf (2020.2-6+b2) ...
Selecting previously unselected package libraqm0:armhf.
Preparing to unpack .../134-libraqm0_0.10.2-1_armhf.deb ...
Unpacking libraqm0:armhf (0.10.2-1) ...
Selecting previously unselected package libsharpyuv0:armhf.
Preparing to unpack .../135-libsharpyuv0_1.4.0-0.1+b1_armhf.deb ...
Unpacking libsharpyuv0:armhf (1.4.0-0.1+b1) ...
Selecting previously unselected package libsm6:armhf.
Preparing to unpack .../136-libsm6_2%3a1.2.4-1_armhf.deb ...
Unpacking libsm6:armhf (2:1.2.4-1) ...
Selecting previously unselected package libwebp7:armhf.
Preparing to unpack .../137-libwebp7_1.4.0-0.1+b1_armhf.deb ...
Unpacking libwebp7:armhf (1.4.0-0.1+b1) ...
Selecting previously unselected package libtiff6:armhf.
Preparing to unpack .../138-libtiff6_4.5.1+git230720-5_armhf.deb ...
Unpacking libtiff6:armhf (4.5.1+git230720-5) ...
Selecting previously unselected package libwebpdemux2:armhf.
Preparing to unpack .../139-libwebpdemux2_1.4.0-0.1+b1_armhf.deb ...
Unpacking libwebpdemux2:armhf (1.4.0-0.1+b1) ...
Selecting previously unselected package libwebpmux3:armhf.
Preparing to unpack .../140-libwebpmux3_1.4.0-0.1+b1_armhf.deb ...
Unpacking libwebpmux3:armhf (1.4.0-0.1+b1) ...
Selecting previously unselected package libxslt1.1:armhf.
Preparing to unpack .../141-libxslt1.1_1.1.35-1.1+b1_armhf.deb ...
Unpacking libxslt1.1:armhf (1.1.35-1.1+b1) ...
Selecting previously unselected package libxt6t64:armhf.
Preparing to unpack .../142-libxt6t64_1%3a1.2.1-1.2+b1_armhf.deb ...
Unpacking libxt6t64:armhf (1:1.2.1-1.2+b1) ...
Selecting previously unselected package libyaml-0-2:armhf.
Preparing to unpack .../143-libyaml-0-2_0.2.5-2_armhf.deb ...
Unpacking libyaml-0-2:armhf (0.2.5-2) ...
Selecting previously unselected package python3-packaging.
Preparing to unpack .../144-python3-packaging_24.2-1_all.deb ...
Unpacking python3-packaging (24.2-1) ...
Selecting previously unselected package python3-pyproject-hooks.
Preparing to unpack .../145-python3-pyproject-hooks_1.2.0-1_all.deb ...
Unpacking python3-pyproject-hooks (1.2.0-1) ...
Selecting previously unselected package python3-toml.
Preparing to unpack .../146-python3-toml_0.10.2-1_all.deb ...
Unpacking python3-toml (0.10.2-1) ...
Selecting previously unselected package python3-wheel.
Preparing to unpack .../147-python3-wheel_0.45.1-1_all.deb ...
Unpacking python3-wheel (0.45.1-1) ...
Selecting previously unselected package python3-build.
Preparing to unpack .../148-python3-build_1.2.2-1_all.deb ...
Unpacking python3-build (1.2.2-1) ...
Selecting previously unselected package python3-installer.
Preparing to unpack .../149-python3-installer_0.7.0+dfsg1-3_all.deb ...
Unpacking python3-installer (0.7.0+dfsg1-3) ...
Selecting previously unselected package pybuild-plugin-pyproject.
Preparing to unpack .../150-pybuild-plugin-pyproject_6.20241217_all.deb ...
Unpacking pybuild-plugin-pyproject (6.20241217) ...
Selecting previously unselected package python-babel-localedata.
Preparing to unpack .../151-python-babel-localedata_2.16.0-1_all.deb ...
Unpacking python-babel-localedata (2.16.0-1) ...
Selecting previously unselected package python-matplotlib-data.
Preparing to unpack .../152-python-matplotlib-data_3.8.3-3_all.deb ...
Unpacking python-matplotlib-data (3.8.3-3) ...
Selecting previously unselected package python3-alabaster.
Preparing to unpack .../153-python3-alabaster_0.7.16-0.1_all.deb ...
Unpacking python3-alabaster (0.7.16-0.1) ...
Selecting previously unselected package python3.13.
Preparing to unpack .../154-python3.13_3.13.1-2_armhf.deb ...
Unpacking python3.13 (3.13.1-2) ...
Selecting previously unselected package python3-all.
Preparing to unpack .../155-python3-all_3.12.8-1_armhf.deb ...
Unpacking python3-all (3.12.8-1) ...
Selecting previously unselected package python3.12-dev.
Preparing to unpack .../156-python3.12-dev_3.12.8-3_armhf.deb ...
Unpacking python3.12-dev (3.12.8-3) ...
Selecting previously unselected package python3-dev.
Preparing to unpack .../157-python3-dev_3.12.8-1_armhf.deb ...
Unpacking python3-dev (3.12.8-1) ...
Selecting previously unselected package python3.13-dev.
Preparing to unpack .../158-python3.13-dev_3.13.1-2_armhf.deb ...
Unpacking python3.13-dev (3.13.1-2) ...
Selecting previously unselected package python3-all-dev.
Preparing to unpack .../159-python3-all-dev_3.12.8-1_armhf.deb ...
Unpacking python3-all-dev (3.12.8-1) ...
Selecting previously unselected package python3-attr.
Preparing to unpack .../160-python3-attr_24.2.0-1_all.deb ...
Unpacking python3-attr (24.2.0-1) ...
Selecting previously unselected package python3-babel.
Preparing to unpack .../161-python3-babel_2.16.0-1_all.deb ...
Unpacking python3-babel (2.16.0-1) ...
Selecting previously unselected package python3-brotli.
Preparing to unpack .../162-python3-brotli_1.1.0-2+b6_armhf.deb ...
Unpacking python3-brotli (1.1.0-2+b6) ...
Selecting previously unselected package python3-certifi.
Preparing to unpack .../163-python3-certifi_2024.8.30+dfsg-1_all.deb ...
Unpacking python3-certifi (2024.8.30+dfsg-1) ...
Selecting previously unselected package python3-chardet.
Preparing to unpack .../164-python3-chardet_5.2.0+dfsg-1_all.deb ...
Unpacking python3-chardet (5.2.0+dfsg-1) ...
Selecting previously unselected package python3-charset-normalizer.
Preparing to unpack .../165-python3-charset-normalizer_3.4.0-1+b1_armhf.deb ...
Unpacking python3-charset-normalizer (3.4.0-1+b1) ...
Selecting previously unselected package python3-numpy.
Preparing to unpack .../166-python3-numpy_1%3a1.26.4+ds-12_armhf.deb ...
Unpacking python3-numpy (1:1.26.4+ds-12) ...
Selecting previously unselected package python3-contourpy.
Preparing to unpack .../167-python3-contourpy_1.3.1-1_armhf.deb ...
Unpacking python3-contourpy (1.3.1-1) ...
Selecting previously unselected package python3-cycler.
Preparing to unpack .../168-python3-cycler_0.12.1-1_all.deb ...
Unpacking python3-cycler (0.12.1-1) ...
Selecting previously unselected package python3-dateutil.
Preparing to unpack .../169-python3-dateutil_2.9.0-3_all.deb ...
Unpacking python3-dateutil (2.9.0-3) ...
Selecting previously unselected package python3-decorator.
Preparing to unpack .../170-python3-decorator_5.1.1-5_all.deb ...
Unpacking python3-decorator (5.1.1-5) ...
Selecting previously unselected package python3-defusedxml.
Preparing to unpack .../171-python3-defusedxml_0.7.1-3_all.deb ...
Unpacking python3-defusedxml (0.7.1-3) ...
Selecting previously unselected package python3-roman.
Preparing to unpack .../172-python3-roman_4.2-1_all.deb ...
Unpacking python3-roman (4.2-1) ...
Selecting previously unselected package python3-docutils.
Preparing to unpack .../173-python3-docutils_0.21.2+dfsg-2_all.deb ...
Unpacking python3-docutils (0.21.2+dfsg-2) ...
Selecting previously unselected package python3-tz.
Preparing to unpack .../174-python3-tz_2024.2-1_all.deb ...
Unpacking python3-tz (2024.2-1) ...
Selecting previously unselected package python3-platformdirs.
Preparing to unpack .../175-python3-platformdirs_4.3.6-1_all.deb ...
Unpacking python3-platformdirs (4.3.6-1) ...
Selecting previously unselected package python3-fs.
Preparing to unpack .../176-python3-fs_2.4.16-5.1_all.deb ...
Unpacking python3-fs (2.4.16-5.1) ...
Selecting previously unselected package python3-lxml:armhf.
Preparing to unpack .../177-python3-lxml_5.3.0-1+b1_armhf.deb ...
Unpacking python3-lxml:armhf (5.3.0-1+b1) ...
Selecting previously unselected package python3-lz4.
Preparing to unpack .../178-python3-lz4_4.4.0+dfsg-1_armhf.deb ...
Unpacking python3-lz4 (4.4.0+dfsg-1) ...
Selecting previously unselected package python3-scipy.
Preparing to unpack .../179-python3-scipy_1.14.1-3_armhf.deb ...
Unpacking python3-scipy (1.14.1-3) ...
Selecting previously unselected package python3-mpmath.
Preparing to unpack .../180-python3-mpmath_1.3.0-1_all.deb ...
Unpacking python3-mpmath (1.3.0-1) ...
Selecting previously unselected package python3-sympy.
Preparing to unpack .../181-python3-sympy_1.13.3-1_all.deb ...
Unpacking python3-sympy (1.13.3-1) ...
Selecting previously unselected package python3-ufolib2.
Preparing to unpack .../182-python3-ufolib2_0.17.0+dfsg1-1_all.deb ...
Unpacking python3-ufolib2 (0.17.0+dfsg1-1) ...
Selecting previously unselected package unicode-data.
Preparing to unpack .../183-unicode-data_15.1.0-1_all.deb ...
Unpacking unicode-data (15.1.0-1) ...
Selecting previously unselected package python3-fonttools.
Preparing to unpack .../184-python3-fonttools_4.55.0-3_armhf.deb ...
Unpacking python3-fonttools (4.55.0-3) ...
Selecting previously unselected package python3-idna.
Preparing to unpack .../185-python3-idna_3.8-2_all.deb ...
Unpacking python3-idna (3.8-2) ...
Selecting previously unselected package python3-imagesize.
Preparing to unpack .../186-python3-imagesize_1.4.1-1_all.deb ...
Unpacking python3-imagesize (1.4.1-1) ...
Selecting previously unselected package python3-iniconfig.
Preparing to unpack .../187-python3-iniconfig_1.1.1-2_all.deb ...
Unpacking python3-iniconfig (1.1.1-2) ...
Selecting previously unselected package python3-markupsafe.
Preparing to unpack .../188-python3-markupsafe_2.1.5-1+b2_armhf.deb ...
Unpacking python3-markupsafe (2.1.5-1+b2) ...
Selecting previously unselected package python3-jinja2.
Preparing to unpack .../189-python3-jinja2_3.1.3-1.1_all.deb ...
Unpacking python3-jinja2 (3.1.3-1.1) ...
Selecting previously unselected package python3-kiwisolver.
Preparing to unpack .../190-python3-kiwisolver_1.4.7-2+b1_armhf.deb ...
Unpacking python3-kiwisolver (1.4.7-2+b1) ...
Selecting previously unselected package python3-pil:armhf.
Preparing to unpack .../191-python3-pil_10.4.0-1+b1_armhf.deb ...
Unpacking python3-pil:armhf (10.4.0-1+b1) ...
Selecting previously unselected package python3.12-tk.
Preparing to unpack .../192-python3.12-tk_3.12.8-3_armhf.deb ...
Unpacking python3.12-tk (3.12.8-3) ...
Selecting previously unselected package python3.13-tk.
Preparing to unpack .../193-python3.13-tk_3.13.1-2_armhf.deb ...
Unpacking python3.13-tk (3.13.1-2) ...
Selecting previously unselected package python3-tk:armhf.
Preparing to unpack .../194-python3-tk_3.13.1-1_armhf.deb ...
Unpacking python3-tk:armhf (3.13.1-1) ...
Selecting previously unselected package python3-pil.imagetk:armhf.
Preparing to unpack .../195-python3-pil.imagetk_10.4.0-1+b1_armhf.deb ...
Unpacking python3-pil.imagetk:armhf (10.4.0-1+b1) ...
Selecting previously unselected package python3-pyparsing.
Preparing to unpack .../196-python3-pyparsing_3.1.2-1_all.deb ...
Unpacking python3-pyparsing (3.1.2-1) ...
Selecting previously unselected package python3-matplotlib.
Preparing to unpack .../197-python3-matplotlib_3.8.3-3+b1_armhf.deb ...
Unpacking python3-matplotlib (3.8.3-3+b1) ...
Selecting previously unselected package sphinx-common.
Preparing to unpack .../198-sphinx-common_8.1.3-3_all.deb ...
Unpacking sphinx-common (8.1.3-3) ...
Selecting previously unselected package python3-pygments.
Preparing to unpack .../199-python3-pygments_2.18.0+dfsg-1_all.deb ...
Unpacking python3-pygments (2.18.0+dfsg-1) ...
Selecting previously unselected package python3-urllib3.
Preparing to unpack .../200-python3-urllib3_2.2.3-4_all.deb ...
Unpacking python3-urllib3 (2.2.3-4) ...
Selecting previously unselected package python3-requests.
Preparing to unpack .../201-python3-requests_2.32.3+dfsg-1_all.deb ...
Unpacking python3-requests (2.32.3+dfsg-1) ...
Selecting previously unselected package python3-snowballstemmer.
Preparing to unpack .../202-python3-snowballstemmer_2.2.0-4_all.deb ...
Unpacking python3-snowballstemmer (2.2.0-4) ...
Selecting previously unselected package python3-sphinx.
Preparing to unpack .../203-python3-sphinx_8.1.3-3_all.deb ...
Unpacking python3-sphinx (8.1.3-3) ...
Selecting previously unselected package python3-tabulate.
Preparing to unpack .../204-python3-tabulate_0.9.0-1_all.deb ...
Unpacking python3-tabulate (0.9.0-1) ...
Selecting previously unselected package python3-numpydoc.
Preparing to unpack .../205-python3-numpydoc_1.8.0-1_all.deb ...
Unpacking python3-numpydoc (1.8.0-1) ...
Selecting previously unselected package python3-pandas-lib:armhf.
Preparing to unpack .../206-python3-pandas-lib_2.2.3+dfsg-5+b1_armhf.deb ...
Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5+b1) ...
Selecting previously unselected package python3-pandas.
Preparing to unpack .../207-python3-pandas_2.2.3+dfsg-5_all.deb ...
Unpacking python3-pandas (2.2.3+dfsg-5) ...
Selecting previously unselected package python3-pluggy.
Preparing to unpack .../208-python3-pluggy_1.5.0-1_all.deb ...
Unpacking python3-pluggy (1.5.0-1) ...
Selecting previously unselected package python3-psutil.
Preparing to unpack .../209-python3-psutil_5.9.8-2_armhf.deb ...
Unpacking python3-psutil (5.9.8-2) ...
Selecting previously unselected package python3-pysam.
Preparing to unpack .../210-python3-pysam_0.22.1+ds-2+b2_armhf.deb ...
Unpacking python3-pysam (0.22.1+ds-2+b2) ...
Selecting previously unselected package python3-pytest.
Preparing to unpack .../211-python3-pytest_8.3.3-1_all.deb ...
Unpacking python3-pytest (8.3.3-1) ...
Selecting previously unselected package python3-yaml.
Preparing to unpack .../212-python3-yaml_6.0.2-1+b1_armhf.deb ...
Unpacking python3-yaml (6.0.2-1+b1) ...
Selecting previously unselected package zip.
Preparing to unpack .../213-zip_3.0-14_armhf.deb ...
Unpacking zip (3.0-14) ...
Selecting previously unselected package unzip.
Preparing to unpack .../214-unzip_6.0-28_armhf.deb ...
Unpacking unzip (6.0-28) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../215-xdg-utils_1.2.1-2_all.deb ...
Unpacking xdg-utils (1.2.1-2) ...
Selecting previously unselected package r-base-core.
Preparing to unpack .../216-r-base-core_4.4.2-1_armhf.deb ...
Unpacking r-base-core (4.4.2-1) ...
Setting up libhtscodecs2:armhf (1.6.1-1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:armhf (1.5.8-1) ...
Setting up libgraphite2-3:armhf (1.3.14-2+b1) ...
Setting up liblcms2-2:armhf (2.16-2) ...
Setting up libpixman-1-0:armhf (0.44.0-3) ...
Setting up libsharpyuv0:armhf (1.4.0-0.1+b1) ...
Setting up libxau6:armhf (1:1.0.11-1) ...
Setting up libxdmcp6:armhf (1:1.1.5-1) ...
Setting up libkeyutils1:armhf (1.6.3-4) ...
Setting up libxcb1:armhf (1.17.0-2+b1) ...
Setting up libicu72:armhf (72.1-5+b1) ...
Setting up liblerc4:armhf (4.0.0+ds-5) ...
Setting up bsdextrautils (2.40.2-12) ...
Setting up libdatrie1:armhf (0.2.13-3+b1) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libxcb-render0:armhf (1.17.0-2+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:armhf (0.2.5-2) ...
Setting up libtirpc-common (1.3.4+ds-1.3) ...
Setting up fonts-lyx (2.4.2.1-1) ...
Setting up unzip (6.0-28) ...
Setting up libdebhelper-perl (13.20) ...
Setting up libbrotli1:armhf (1.1.0-2+b6) ...
Setting up libmagic1t64:armhf (1:5.45-3+b1) ...
Setting up x11-common (1:7.7+23.1) ...
invoke-rc.d: could not determine current runlevel
Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libpsl5t64:armhf (0.21.2-1.1+b1) ...
Setting up libnghttp2-14:armhf (1.64.0-1) ...
Setting up libdeflate0:armhf (1.22-1) ...
Setting up gettext-base (0.22.5-3) ...
Setting up m4 (1.4.19-4) ...
Setting up libqhull-r8.0:armhf (2020.2-6+b2) ...
Setting up libxcb-shm0:armhf (1.17.0-2+b1) ...
Setting up libcom-err2:armhf (1.47.2~rc1-2) ...
Setting up file (1:5.45-3+b1) ...
Setting up libjbig0:armhf (2.1-6.1+b2) ...
Setting up libelf1t64:armhf (0.192-4) ...
Setting up python-babel-localedata (2.16.0-1) ...
Setting up libkrb5support0:armhf (1.21.3-3) ...
Setting up libsasl2-modules-db:armhf (2.1.28+dfsg1-8) ...
Setting up tzdata (2024b-4) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Mon Dec 30 23:02:45 UTC 2024.
Universal Time is now:  Mon Dec 30 23:02:45 UTC 2024.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up unicode-data (15.1.0-1) ...
Setting up libpython3.13-minimal:armhf (3.13.1-2) ...
Setting up zip (3.0-14) ...
Setting up autotools-dev (20220109.1) ...
Setting up libglib2.0-0t64:armhf (2.82.4-1) ...
No schema files found: doing nothing.
Setting up libblas3:armhf (3.12.0-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libexpat1-dev:armhf (2.6.4-1) ...
Setting up libjpeg62-turbo:armhf (1:2.1.5-3+b1) ...
Setting up libx11-data (2:1.8.10-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libfribidi0:armhf (1.0.16-1) ...
Setting up libimagequant0:armhf (2.18.0-1+b2) ...
Setting up libproc2-0:armhf (2:4.0.4-6) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16t64:armhf (1.6.44-3) ...
Setting up libtcl8.6:armhf (8.6.15+dfsg-2) ...
Setting up autopoint (0.22.5-3) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libk5crypto3:armhf (1.21.3-3) ...
Setting up libsasl2-2:armhf (2.1.28+dfsg1-8) ...
Setting up libgfortran5:armhf (14.2.0-8) ...
Setting up autoconf (2.72-3) ...
Setting up libnghttp3-9:armhf (1.6.0-2) ...
Setting up libwebp7:armhf (1.4.0-0.1+b1) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b2) ...
Setting up sensible-utils (0.0.24) ...
Setting up libtiff6:armhf (4.5.1+git230720-5) ...
Setting up libuchardet0:armhf (0.0.8-1+b2) ...
Setting up procps (2:4.0.4-6) ...
Setting up libjson-perl (4.10000-1) ...
Setting up libopenjp2-7:armhf (2.5.0-2+b4) ...
Setting up python3.13-minimal (3.13.1-2) ...
Setting up libx11-6:armhf (2:1.8.10-2) ...
Setting up libthai-data (0.1.29-2) ...
Setting up netbase (6.4) ...
Setting up libngtcp2-16:armhf (1.9.1-1) ...
Setting up sgml-base (1.31) ...
Setting up libkrb5-3:armhf (1.21.3-3) ...
Setting up libpaper2:armhf (2.2.5-0.3) ...
Setting up libssh2-1t64:armhf (1.11.1-1) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up python-matplotlib-data (3.8.3-3) ...
Setting up openssl (3.3.2-2) ...
Setting up libwebpmux3:armhf (1.4.0-0.1+b1) ...
Setting up readline-common (8.2-6) ...
Setting up libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ...
Setting up xdg-utils (1.2.1-2) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up bedtools (2.31.1+dfsg-2) ...
Setting up libngtcp2-crypto-gnutls8:armhf (1.9.1-1) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up libice6:armhf (2:1.1.1-1) ...
Setting up liblapack3:armhf (3.12.0-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up gettext (0.22.5-3) ...
Setting up libxrender1:armhf (1:0.9.10-1.1+b3) ...
Setting up libtool (2.4.7-8) ...
Setting up fontconfig-config (2.15.0-1.1+b1) ...
Setting up libwebpdemux2:armhf (1.4.0-0.1+b1) ...
Setting up libxext6:armhf (2:1.3.4-1+b2) ...
Setting up libpaper-utils (2.2.5-0.3) ...
Setting up libldap-2.5-0:armhf (2.5.19+dfsg-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libthai0:armhf (0.1.29-2+b1) ...
Setting up ca-certificates (20240203) ...
Updating certificates in /etc/ssl/certs...
146 added, 0 removed; done.
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up libfreetype6:armhf (2.13.3+dfsg-1) ...
Setting up libgssapi-krb5-2:armhf (1.21.3-3) ...
Setting up ucf (3.0046) ...
Setting up libjs-sphinxdoc (8.1.3-3) ...
Setting up libreadline8t64:armhf (8.2-6) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-6) ...
Setting up xml-core (0.19) ...
Setting up libxslt1.1:armhf (1.1.35-1.1+b1) ...
Setting up libharfbuzz0b:armhf (10.1.0-1) ...
Setting up libxss1:armhf (1:1.2.3-1+b2) ...
Setting up libfontconfig1:armhf (2.15.0-1.1+b1) ...
Setting up libsm6:armhf (2:1.2.4-1) ...
Setting up libpython3.13-stdlib:armhf (3.13.1-2) ...
Setting up liblbfgsb0:armhf (3.0+dfsg.4-1+b2) ...
Setting up libpython3.13:armhf (3.13.1-2) ...
Setting up fontconfig (2.15.0-1.1+b1) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.6-1+b3) ...
Setting up libcurl4t64:armhf (8.11.1-1) ...
Setting up libtirpc3t64:armhf (1.3.4+ds-1.3+b1) ...
Setting up python3.13 (3.13.1-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libtk8.6:armhf (8.6.15-1) ...
Setting up libpango-1.0-0:armhf (1.55.0+ds-3) ...
Setting up python3.12-tk (3.12.8-3) ...
Setting up libcurl3t64-gnutls:armhf (8.11.1-1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:armhf (1.18.2-2) ...
Setting up python3.13-tk (3.13.1-2) ...
Setting up libraqm0:armhf (0.10.2-1) ...
Setting up libpython3.13-dev:armhf (3.13.1-2) ...
Setting up sphinx-common (8.1.3-3) ...
Setting up libxt6t64:armhf (1:1.2.1-1.2+b1) ...
Setting up libnsl2:armhf (1.3.0-3+b3) ...
Setting up libhts3t64:armhf (1.20+ds-2) ...
Setting up libpangoft2-1.0-0:armhf (1.55.0+ds-3) ...
Setting up libpangocairo-1.0-0:armhf (1.55.0+ds-3) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ...
Setting up libpython3.12-stdlib:armhf (3.12.8-3) ...
Setting up python3.13-dev (3.13.1-2) ...
Setting up blt (2.5.3+dfsg-7) ...
Setting up python3.12 (3.12.8-3) ...
Setting up debhelper (13.20) ...
Setting up libpython3.12t64:armhf (3.12.8-3) ...
Setting up r-base-core (4.4.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up libpython3-stdlib:armhf (3.12.8-1) ...
Setting up python3 (3.12.8-1) ...
Setting up libpython3.12-dev:armhf (3.12.8-3) ...
Setting up python3-zipp (3.21.0-1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up python3-markupsafe (2.1.5-1+b2) ...
Setting up python3-wheel (0.45.1-1) ...
Setting up python3-platformdirs (4.3.6-1) ...
Setting up python3-psutil (5.9.8-2) ...
Setting up python3-tz (2024.2-1) ...
Setting up python3-pil:armhf (10.4.0-1+b1) ...
Setting up python3-roman (4.2-1) ...
Setting up python3-decorator (5.1.1-5) ...
Setting up python3-jinja2 (3.1.3-1.1) ...
Setting up python3-packaging (24.2-1) ...
Setting up python3-pyproject-hooks (1.2.0-1) ...
Setting up python3-pyparsing (3.1.2-1) ...
Setting up python3-certifi (2024.8.30+dfsg-1) ...
Setting up python3-snowballstemmer (2.2.0-4) ...
Setting up python3-brotli (1.1.0-2+b6) ...
Setting up python3-cycler (0.12.1-1) ...
Setting up python3-kiwisolver (1.4.7-2+b1) ...
Setting up python3-idna (3.8-2) ...
Setting up python3.12-dev (3.12.8-3) ...
Setting up cython3 (3.0.11+dfsg-1+b1) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up python3-toml (0.10.2-1) ...
Setting up python3-installer (0.7.0+dfsg1-3) ...
Setting up python3-urllib3 (2.2.3-4) ...
Setting up python3-pluggy (1.5.0-1) ...
Setting up python3-lxml:armhf (5.3.0-1+b1) ...
Setting up python3-dateutil (2.9.0-3) ...
Setting up python3-mpmath (1.3.0-1) ...
Setting up python3-build (1.2.2-1) ...
Setting up python3-imagesize (1.4.1-1) ...
Setting up python3-more-itertools (10.5.0-1) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-sympy (1.13.3-1) ...
Setting up python3-attr (24.2.0-1) ...
Setting up python3-pysam (0.22.1+ds-2+b2) ...
Setting up libpython3-dev:armhf (3.12.8-1) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up python3-jaraco.context (6.0.0-1) ...
Setting up python3-lz4 (4.4.0+dfsg-1) ...
Setting up python3-defusedxml (0.7.1-3) ...
Setting up python3-charset-normalizer (3.4.0-1+b1) ...
Setting up python3-pytest (8.3.3-1) ...
Setting up python3-alabaster (0.7.16-0.1) ...
Setting up python3-typeguard (4.4.1-1) ...
Setting up python3-tabulate (0.9.0-1) ...
Setting up python3-all (3.12.8-1) ...
Setting up python3-yaml (6.0.2-1+b1) ...
Setting up python3-tk:armhf (3.13.1-1) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-pil.imagetk:armhf (10.4.0-1+b1) ...
Setting up libpython3-all-dev:armhf (3.12.8-1) ...
Setting up python3-jaraco.text (4.0.0-1) ...
Setting up python3-dev (3.12.8-1) ...
Setting up python3-pkg-resources (75.6.0-1) ...
Setting up python3-all-dev (3.12.8-1) ...
Setting up python3-setuptools (75.6.0-1) ...
Setting up python3-babel (2.16.0-1) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-fs (2.4.16-5.1) ...
Setting up python3-pygments (2.18.0+dfsg-1) ...
Setting up python3-chardet (5.2.0+dfsg-1) ...
Setting up python3-requests (2.32.3+dfsg-1) ...
Setting up python3-numpy (1:1.26.4+ds-12) ...
Setting up python3-contourpy (1.3.1-1) ...
Setting up dh-python (6.20241217) ...
Setting up python3-scipy (1.14.1-3) ...
Setting up pybuild-plugin-pyproject (6.20241217) ...
Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5+b1) ...
Setting up python3-pandas (2.2.3+dfsg-5) ...
Setting up python3-fonttools (4.55.0-3) ...
Setting up python3-ufolib2 (0.17.0+dfsg1-1) ...
Setting up python3-matplotlib (3.8.3-3+b1) ...
Processing triggers for libc-bin (2.40-4) ...
Processing triggers for sgml-base (1.31) ...
Setting up docutils-common (0.21.2+dfsg-2) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.21.2+dfsg-2) ...
Setting up python3-sphinx (8.1.3-3) ...
Setting up python3-numpydoc (1.8.0-1) ...
Processing triggers for ca-certificates (20240203) ...
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: user script /srv/workspace/pbuilder/12153/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for trixie
I: user script /srv/workspace/pbuilder/12153/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/python-pybedtools-0.10.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../python-pybedtools_0.10.0-4_source.changes
dpkg-buildpackage: info: source package python-pybedtools
dpkg-buildpackage: info: source version 0.10.0-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from python-pybedtools-0.10.0/debian/source/options: --extend-diff-ignore=(pybedtools/version.py|docs/source/pybedtools.featurefuncs.*.rst)
 debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0'
/bin/rm -rf fakehome .eggs .pybuild .pytest_cache
/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
rm -rf docs/build docs/*.bed docs/*.genome
rm -rf dist
/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/reproducible-path/python-pybedtools-0.10.0'
   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
   dh_auto_build -O--buildsystem=pybuild
I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module
I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools  
* Building wheel...
<string>:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running bdist_wheel
The [wheel] section is deprecated. Use [bdist_wheel] instead.
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:111: SetuptoolsDeprecationWarning: bdist_wheel.universal is deprecated
!!

        ********************************************************************************
        With Python 2.7 end-of-life, support for building universal wheels
        (i.e., wheels that support both Python 2 and Python 3)
        is being obviated.
        Please discontinue using this option, or if you still need it,
        file an issue with pypa/setuptools describing your use case.

        By 2025-Aug-30, you need to update your project and remove deprecated calls
        or your builds will no longer be supported.
        ********************************************************************************

!!
  self.finalize_options()
running build
running build_py
creating build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/paths.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-313/pybedtools
creating build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_issues.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_1.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-313/pybedtools/test
creating build/lib.linux-armv7l-cpython-313/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-313/pybedtools/contrib
creating build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-313/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:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'pybedtools.include' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'pybedtools.include' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'pybedtools.include' to be distributed and are
        already explicitly excluding 'pybedtools.include' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools
copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-313/pybedtools
creating build/lib.linux-armv7l-cpython-313/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include
copying pybedtools/include/bedFile.h -> build/lib.linux-armv7l-cpython-313/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include
copying pybedtools/include/fileType.h -> build/lib.linux-armv7l-cpython-313/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-armv7l-cpython-313/pybedtools/include
copying pybedtools/include/gzstream.h -> build/lib.linux-armv7l-cpython-313/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-armv7l-cpython-313/pybedtools/include
copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-313/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/mpl-expected.png -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_cases.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-armv7l-cpython-313/pybedtools/test
running build_ext
Trying to generate the following missing files:
pybedtools/cbedtools.cpp
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/cbedtools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
Compiling pybedtools/cbedtools.pyx because it changed.
[1/1] Cythonizing pybedtools/cbedtools.pyx
Trying to generate the following missing files:
pybedtools/featurefuncs.cpp
Compiling pybedtools/featurefuncs.pyx because it changed.
[1/1] Cythonizing pybedtools/featurefuncs.pyx
building 'pybedtools.cbedtools' extension
creating build/temp.linux-armv7l-cpython-313/pybedtools
creating build/temp.linux-armv7l-cpython-313/pybedtools/include
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/cbedtools.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/cbedtools.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/include/bedFile.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/include/fileType.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-313/pybedtools/cbedtools.o build/temp.linux-armv7l-cpython-313/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-313/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o build/lib.linux-armv7l-cpython-313/pybedtools/cbedtools.cpython-313-arm-linux-gnueabihf.so
building 'pybedtools.featurefuncs' extension
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/featurefuncs.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/featurefuncs.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/include/bedFile.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/include/fileType.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-313/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-313/pybedtools/featurefuncs.o build/temp.linux-armv7l-cpython-313/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-313/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o build/lib.linux-armv7l-cpython-313/pybedtools/featurefuncs.cpython-313-arm-linux-gnueabihf.so
installing to build/bdist.linux-armv7l/wheel
running install
running install_lib
creating build/bdist.linux-armv7l/wheel
creating build/bdist.linux-armv7l/wheel/pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/helpers.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/_Window.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/paths.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/cbedtools.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/parallel.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/featurefuncs.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/settings.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/stats.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/bedtool.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/genome_registry.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/filenames.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/cbedtools.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools
creating build/bdist.linux-armv7l/wheel/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-313/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-313/pybedtools/contrib/plotting.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-313/pybedtools/contrib/bigwig.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-313/pybedtools/contrib/venn_maker.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-313/pybedtools/contrib/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-313/pybedtools/contrib/bigbed.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-313/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-313/pybedtools/logger.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools
creating build/bdist.linux-armv7l/wheel/pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_contrib.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_len_leak.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_issues.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_cases.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/genomepy_integration.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_gzip_support.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_iter.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_cbedtools.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/gchart-expected.png -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_1.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_merge215.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/regression_tests.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/mpl-expected.png -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_merge227.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
creating build/bdist.linux-armv7l/wheel/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/x.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/y.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/x.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/bedpe.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/reads.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/small.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/issue_121.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/164.gtf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/b.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/small.fastq -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/test.fa.fai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/v.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/c.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/m1.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/genome.fa -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/issue319.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/a.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.cram -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/test.fa -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/d.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/a.igv_script -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/venn.b.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/exons.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/expand_test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/a.links.html -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/venn.c.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/hg19.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_pathlib.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/test_helpers.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-313/pybedtools/test/tfuncs.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
creating build/bdist.linux-armv7l/wheel/pybedtools/include
copying build/lib.linux-armv7l-cpython-313/pybedtools/include/bedFile.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-313/pybedtools/include/fileType.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-313/pybedtools/include/gzstream.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-313/pybedtools/include/bedFile.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-313/pybedtools/include/fileType.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-313/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-313/pybedtools/include/gzstream.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-313/pybedtools/featurefuncs.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/cbedtools.pxd -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-313/pybedtools/version.py -> build/bdist.linux-armv7l/wheel/./pybedtools
running install_egg_info
Copying pybedtools.egg-info to build/bdist.linux-armv7l/wheel/./pybedtools-0.10.0.egg-info
running install_scripts
creating build/bdist.linux-armv7l/wheel/pybedtools-0.10.0.dist-info/WHEEL
creating '/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/.tmp-zhwyes7c/pybedtools-0.10.0-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
adding 'pybedtools/_Window.pyx'
adding 'pybedtools/__init__.py'
adding 'pybedtools/bedtool.py'
adding 'pybedtools/cbedtools.cpython-313-arm-linux-gnueabihf.so'
adding 'pybedtools/cbedtools.pxd'
adding 'pybedtools/cbedtools.pyx'
adding 'pybedtools/featurefuncs.cpython-313-arm-linux-gnueabihf.so'
adding 'pybedtools/featurefuncs.pyx'
adding 'pybedtools/filenames.py'
adding 'pybedtools/genome_registry.py'
adding 'pybedtools/helpers.py'
adding 'pybedtools/logger.py'
adding 'pybedtools/parallel.py'
adding 'pybedtools/paths.py'
adding 'pybedtools/settings.py'
adding 'pybedtools/stats.py'
adding 'pybedtools/version.py'
adding 'pybedtools/contrib/__init__.py'
adding 'pybedtools/contrib/bigbed.py'
adding 'pybedtools/contrib/bigwig.py'
adding 'pybedtools/contrib/intersection_matrix.py'
adding 'pybedtools/contrib/long_range_interaction.py'
adding 'pybedtools/contrib/plotting.py'
adding 'pybedtools/contrib/venn_maker.py'
adding 'pybedtools/include/bedFile.cpp'
adding 'pybedtools/include/bedFile.h'
adding 'pybedtools/include/fileType.cpp'
adding 'pybedtools/include/fileType.h'
adding 'pybedtools/include/gzstream.cpp'
adding 'pybedtools/include/gzstream.h'
adding 'pybedtools/include/lineFileUtilities.h'
adding 'pybedtools/test/__init__.py'
adding 'pybedtools/test/gchart-expected.png'
adding 'pybedtools/test/genomepy_integration.py'
adding 'pybedtools/test/mpl-expected.png'
adding 'pybedtools/test/prevent_open_file_regression'
adding 'pybedtools/test/regression_tests.py'
adding 'pybedtools/test/test_1.py'
adding 'pybedtools/test/test_cases.yaml'
adding 'pybedtools/test/test_cbedtools.py'
adding 'pybedtools/test/test_contrib.py'
adding 'pybedtools/test/test_gzip_support.py'
adding 'pybedtools/test/test_helpers.py'
adding 'pybedtools/test/test_issues.py'
adding 'pybedtools/test/test_iter.py'
adding 'pybedtools/test/test_len_leak.py'
adding 'pybedtools/test/test_merge215.yaml'
adding 'pybedtools/test/test_merge227.yaml'
adding 'pybedtools/test/test_pathlib.py'
adding 'pybedtools/test/test_shuffle215.yaml'
adding 'pybedtools/test/test_shuffle227.yaml'
adding 'pybedtools/test/tfuncs.py'
adding 'pybedtools/test/data/1000genomes-example.vcf'
adding 'pybedtools/test/data/164.gtf'
adding 'pybedtools/test/data/BEAF_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/CTCF_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/Cp190_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/SuHw_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/__init__.py'
adding 'pybedtools/test/data/a.bed'
adding 'pybedtools/test/data/a.igv_script'
adding 'pybedtools/test/data/a.links.html'
adding 'pybedtools/test/data/b.bed'
adding 'pybedtools/test/data/bedpe.bed'
adding 'pybedtools/test/data/bedpe2.bed'
adding 'pybedtools/test/data/c.gff'
adding 'pybedtools/test/data/d.gff'
adding 'pybedtools/test/data/democonfig.yaml'
adding 'pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz'
adding 'pybedtools/test/data/dm3-chr2L-5M.gff.gz'
adding 'pybedtools/test/data/example.narrowPeak'
adding 'pybedtools/test/data/exons.gff'
adding 'pybedtools/test/data/expand_test.bed'
adding 'pybedtools/test/data/gdc.1.100.bam'
adding 'pybedtools/test/data/gdc.1.100.bam.bai'
adding 'pybedtools/test/data/gdc.50.200.bam'
adding 'pybedtools/test/data/gdc.50.200.bam.bai'
adding 'pybedtools/test/data/gdc.bam'
adding 'pybedtools/test/data/gdc.bed'
adding 'pybedtools/test/data/gdc.cram'
adding 'pybedtools/test/data/gdc.gff'
adding 'pybedtools/test/data/gdc.gff.gz'
adding 'pybedtools/test/data/gdc.othersort.bam'
adding 'pybedtools/test/data/gdc.sorted.bam'
adding 'pybedtools/test/data/gdc.sorted.bam.bai'
adding 'pybedtools/test/data/genome.fa'
adding 'pybedtools/test/data/hg19.gff'
adding 'pybedtools/test/data/hg38-base.bed'
adding 'pybedtools/test/data/hg38-problem.bed'
adding 'pybedtools/test/data/issue319.bed'
adding 'pybedtools/test/data/issue319.out.bed'
adding 'pybedtools/test/data/issue319.vcf.gz'
adding 'pybedtools/test/data/issue_121.bam'
adding 'pybedtools/test/data/m1.bed'
adding 'pybedtools/test/data/mm9.bed12'
adding 'pybedtools/test/data/multibamcov_test.bed'
adding 'pybedtools/test/data/reads.bam'
adding 'pybedtools/test/data/rmsk.hg18.chr21.small.bed'
adding 'pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz'
adding 'pybedtools/test/data/small.bam'
adding 'pybedtools/test/data/small.fastq'
adding 'pybedtools/test/data/snps.bed.gz'
adding 'pybedtools/test/data/tag_test1.bed'
adding 'pybedtools/test/data/tag_test2.bed'
adding 'pybedtools/test/data/test.fa'
adding 'pybedtools/test/data/test.fa.fai'
adding 'pybedtools/test/data/test_bedpe.bed'
adding 'pybedtools/test/data/test_peaks.bed'
adding 'pybedtools/test/data/test_tsses.bed'
adding 'pybedtools/test/data/v.vcf'
adding 'pybedtools/test/data/vcf-stderr-test.bed'
adding 'pybedtools/test/data/vcf-stderr-test.vcf'
adding 'pybedtools/test/data/venn.b.bed'
adding 'pybedtools/test/data/venn.c.bed'
adding 'pybedtools/test/data/x.bam'
adding 'pybedtools/test/data/x.bed'
adding 'pybedtools/test/data/y.bam'
adding 'pybedtools-0.10.0.dist-info/LICENSE.txt'
adding 'pybedtools-0.10.0.dist-info/METADATA'
adding 'pybedtools-0.10.0.dist-info/WHEEL'
adding 'pybedtools-0.10.0.dist-info/top_level.txt'
adding 'pybedtools-0.10.0.dist-info/RECORD'
removing build/bdist.linux-armv7l/wheel
Successfully built pybedtools-0.10.0-cp313-cp313-linux_armv7l.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module
I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module
I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools  
* Building wheel...
<string>:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running bdist_wheel
The [wheel] section is deprecated. Use [bdist_wheel] instead.
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:111: SetuptoolsDeprecationWarning: bdist_wheel.universal is deprecated
!!

        ********************************************************************************
        With Python 2.7 end-of-life, support for building universal wheels
        (i.e., wheels that support both Python 2 and Python 3)
        is being obviated.
        Please discontinue using this option, or if you still need it,
        file an issue with pypa/setuptools describing your use case.

        By 2025-Aug-30, you need to update your project and remove deprecated calls
        or your builds will no longer be supported.
        ********************************************************************************

!!
  self.finalize_options()
running build
running build_py
creating build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/helpers.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/paths.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/parallel.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/settings.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/stats.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/logger.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/__init__.py -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/version.py -> build/lib.linux-armv7l-cpython-312/pybedtools
creating build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_contrib.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_issues.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/__init__.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_1.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/regression_tests.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_helpers.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test
creating build/lib.linux-armv7l-cpython-312/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-armv7l-cpython-312/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-312/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-312/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-312/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-312/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-312/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-312/pybedtools/contrib
creating build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
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:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration.
!!

        ********************************************************************************
        ############################
        # Package would be ignored #
        ############################
        Python recognizes 'pybedtools.include' as an importable package[^1],
        but it is absent from setuptools' `packages` configuration.

        This leads to an ambiguous overall configuration. If you want to distribute this
        package, please make sure that 'pybedtools.include' is explicitly added
        to the `packages` configuration field.

        Alternatively, you can also rely on setuptools' discovery methods
        (for example by using `find_namespace_packages(...)`/`find_namespace:`
        instead of `find_packages(...)`/`find:`).

        You can read more about "package discovery" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

        If you don't want 'pybedtools.include' to be distributed and are
        already explicitly excluding 'pybedtools.include' via
        `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
        you can try to use `exclude_package_data`, or `include-package-data=False` in
        combination with a more fine grained `package-data` configuration.

        You can read more about "package data files" on setuptools documentation page:

        - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


        [^1]: For Python, any directory (with suitable naming) can be imported,
              even if it does not contain any `.py` files.
              On the other hand, currently there is no concept of package data
              directory, all directories are treated like packages.
        ********************************************************************************

!!
  check.warn(importable)
copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/cbedtools.cpp -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/featurefuncs.cpp -> build/lib.linux-armv7l-cpython-312/pybedtools
copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-312/pybedtools
creating build/lib.linux-armv7l-cpython-312/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-armv7l-cpython-312/pybedtools/include
copying pybedtools/include/bedFile.h -> build/lib.linux-armv7l-cpython-312/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-armv7l-cpython-312/pybedtools/include
copying pybedtools/include/fileType.h -> build/lib.linux-armv7l-cpython-312/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-armv7l-cpython-312/pybedtools/include
copying pybedtools/include/gzstream.h -> build/lib.linux-armv7l-cpython-312/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-armv7l-cpython-312/pybedtools/include
copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-312/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/mpl-expected.png -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_cases.yaml -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-armv7l-cpython-312/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-armv7l-cpython-312/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
creating build/temp.linux-armv7l-cpython-312/pybedtools
creating build/temp.linux-armv7l-cpython-312/pybedtools/include
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-armv7l-cpython-312/pybedtools/cbedtools.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-312/pybedtools/include/bedFile.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-312/pybedtools/include/fileType.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-312/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/pybedtools/cbedtools.o build/temp.linux-armv7l-cpython-312/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-312/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o build/lib.linux-armv7l-cpython-312/pybedtools/cbedtools.cpython-312-arm-linux-gnueabihf.so
building 'pybedtools.featurefuncs' extension
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-armv7l-cpython-312/pybedtools/featurefuncs.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-312/pybedtools/include/bedFile.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-312/pybedtools/include/fileType.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-312/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-312/pybedtools/featurefuncs.o build/temp.linux-armv7l-cpython-312/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-312/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o build/lib.linux-armv7l-cpython-312/pybedtools/featurefuncs.cpython-312-arm-linux-gnueabihf.so
installing to build/bdist.linux-armv7l/wheel
running install
running install_lib
creating build/bdist.linux-armv7l/wheel
creating build/bdist.linux-armv7l/wheel/pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/helpers.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/_Window.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/featurefuncs.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/paths.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/parallel.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/settings.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/stats.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/bedtool.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/cbedtools.cpython-312-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/genome_registry.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/filenames.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/cbedtools.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/cbedtools.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools
creating build/bdist.linux-armv7l/wheel/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-312/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-312/pybedtools/contrib/plotting.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-312/pybedtools/contrib/bigwig.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-312/pybedtools/contrib/venn_maker.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-312/pybedtools/contrib/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-312/pybedtools/contrib/bigbed.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-312/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-armv7l/wheel/./pybedtools/contrib
copying build/lib.linux-armv7l-cpython-312/pybedtools/logger.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools
creating build/bdist.linux-armv7l/wheel/pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_contrib.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_len_leak.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_issues.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_cases.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/genomepy_integration.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_gzip_support.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_iter.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_cbedtools.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/gchart-expected.png -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_1.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_merge215.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/regression_tests.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/mpl-expected.png -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_merge227.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test
creating build/bdist.linux-armv7l/wheel/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/x.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/y.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/x.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/bedpe.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/reads.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/small.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/issue_121.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/164.gtf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/b.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/small.fastq -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/test.fa.fai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/v.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/c.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/m1.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/genome.fa -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/issue319.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/a.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.cram -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/__init__.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/test.fa -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/d.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/a.igv_script -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/venn.b.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/exons.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/expand_test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/a.links.html -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/venn.c.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/hg19.gff -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-armv7l/wheel/./pybedtools/test/data
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_pathlib.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/test_helpers.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
copying build/lib.linux-armv7l-cpython-312/pybedtools/test/tfuncs.py -> build/bdist.linux-armv7l/wheel/./pybedtools/test
creating build/bdist.linux-armv7l/wheel/pybedtools/include
copying build/lib.linux-armv7l-cpython-312/pybedtools/include/bedFile.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-312/pybedtools/include/fileType.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-312/pybedtools/include/gzstream.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-312/pybedtools/include/bedFile.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-312/pybedtools/include/fileType.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-312/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-312/pybedtools/include/gzstream.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools/include
copying build/lib.linux-armv7l-cpython-312/pybedtools/featurefuncs.pyx -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/cbedtools.pxd -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/version.py -> build/bdist.linux-armv7l/wheel/./pybedtools
copying build/lib.linux-armv7l-cpython-312/pybedtools/featurefuncs.cpp -> build/bdist.linux-armv7l/wheel/./pybedtools
running install_egg_info
Copying pybedtools.egg-info to build/bdist.linux-armv7l/wheel/./pybedtools-0.10.0.egg-info
running install_scripts
creating build/bdist.linux-armv7l/wheel/pybedtools-0.10.0.dist-info/WHEEL
creating '/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/.tmp-dub7ddad/pybedtools-0.10.0-cp312-cp312-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
adding 'pybedtools/_Window.pyx'
adding 'pybedtools/__init__.py'
adding 'pybedtools/bedtool.py'
adding 'pybedtools/cbedtools.cpp'
adding 'pybedtools/cbedtools.cpython-312-arm-linux-gnueabihf.so'
adding 'pybedtools/cbedtools.pxd'
adding 'pybedtools/cbedtools.pyx'
adding 'pybedtools/featurefuncs.cpp'
adding 'pybedtools/featurefuncs.cpython-312-arm-linux-gnueabihf.so'
adding 'pybedtools/featurefuncs.pyx'
adding 'pybedtools/filenames.py'
adding 'pybedtools/genome_registry.py'
adding 'pybedtools/helpers.py'
adding 'pybedtools/logger.py'
adding 'pybedtools/parallel.py'
adding 'pybedtools/paths.py'
adding 'pybedtools/settings.py'
adding 'pybedtools/stats.py'
adding 'pybedtools/version.py'
adding 'pybedtools/contrib/__init__.py'
adding 'pybedtools/contrib/bigbed.py'
adding 'pybedtools/contrib/bigwig.py'
adding 'pybedtools/contrib/intersection_matrix.py'
adding 'pybedtools/contrib/long_range_interaction.py'
adding 'pybedtools/contrib/plotting.py'
adding 'pybedtools/contrib/venn_maker.py'
adding 'pybedtools/include/bedFile.cpp'
adding 'pybedtools/include/bedFile.h'
adding 'pybedtools/include/fileType.cpp'
adding 'pybedtools/include/fileType.h'
adding 'pybedtools/include/gzstream.cpp'
adding 'pybedtools/include/gzstream.h'
adding 'pybedtools/include/lineFileUtilities.h'
adding 'pybedtools/test/__init__.py'
adding 'pybedtools/test/gchart-expected.png'
adding 'pybedtools/test/genomepy_integration.py'
adding 'pybedtools/test/mpl-expected.png'
adding 'pybedtools/test/prevent_open_file_regression'
adding 'pybedtools/test/regression_tests.py'
adding 'pybedtools/test/test_1.py'
adding 'pybedtools/test/test_cases.yaml'
adding 'pybedtools/test/test_cbedtools.py'
adding 'pybedtools/test/test_contrib.py'
adding 'pybedtools/test/test_gzip_support.py'
adding 'pybedtools/test/test_helpers.py'
adding 'pybedtools/test/test_issues.py'
adding 'pybedtools/test/test_iter.py'
adding 'pybedtools/test/test_len_leak.py'
adding 'pybedtools/test/test_merge215.yaml'
adding 'pybedtools/test/test_merge227.yaml'
adding 'pybedtools/test/test_pathlib.py'
adding 'pybedtools/test/test_shuffle215.yaml'
adding 'pybedtools/test/test_shuffle227.yaml'
adding 'pybedtools/test/tfuncs.py'
adding 'pybedtools/test/data/1000genomes-example.vcf'
adding 'pybedtools/test/data/164.gtf'
adding 'pybedtools/test/data/BEAF_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/CTCF_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/Cp190_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/SuHw_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/__init__.py'
adding 'pybedtools/test/data/a.bed'
adding 'pybedtools/test/data/a.igv_script'
adding 'pybedtools/test/data/a.links.html'
adding 'pybedtools/test/data/b.bed'
adding 'pybedtools/test/data/bedpe.bed'
adding 'pybedtools/test/data/bedpe2.bed'
adding 'pybedtools/test/data/c.gff'
adding 'pybedtools/test/data/d.gff'
adding 'pybedtools/test/data/democonfig.yaml'
adding 'pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz'
adding 'pybedtools/test/data/dm3-chr2L-5M.gff.gz'
adding 'pybedtools/test/data/example.narrowPeak'
adding 'pybedtools/test/data/exons.gff'
adding 'pybedtools/test/data/expand_test.bed'
adding 'pybedtools/test/data/gdc.1.100.bam'
adding 'pybedtools/test/data/gdc.1.100.bam.bai'
adding 'pybedtools/test/data/gdc.50.200.bam'
adding 'pybedtools/test/data/gdc.50.200.bam.bai'
adding 'pybedtools/test/data/gdc.bam'
adding 'pybedtools/test/data/gdc.bed'
adding 'pybedtools/test/data/gdc.cram'
adding 'pybedtools/test/data/gdc.gff'
adding 'pybedtools/test/data/gdc.gff.gz'
adding 'pybedtools/test/data/gdc.othersort.bam'
adding 'pybedtools/test/data/gdc.sorted.bam'
adding 'pybedtools/test/data/gdc.sorted.bam.bai'
adding 'pybedtools/test/data/genome.fa'
adding 'pybedtools/test/data/hg19.gff'
adding 'pybedtools/test/data/hg38-base.bed'
adding 'pybedtools/test/data/hg38-problem.bed'
adding 'pybedtools/test/data/issue319.bed'
adding 'pybedtools/test/data/issue319.out.bed'
adding 'pybedtools/test/data/issue319.vcf.gz'
adding 'pybedtools/test/data/issue_121.bam'
adding 'pybedtools/test/data/m1.bed'
adding 'pybedtools/test/data/mm9.bed12'
adding 'pybedtools/test/data/multibamcov_test.bed'
adding 'pybedtools/test/data/reads.bam'
adding 'pybedtools/test/data/rmsk.hg18.chr21.small.bed'
adding 'pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz'
adding 'pybedtools/test/data/small.bam'
adding 'pybedtools/test/data/small.fastq'
adding 'pybedtools/test/data/snps.bed.gz'
adding 'pybedtools/test/data/tag_test1.bed'
adding 'pybedtools/test/data/tag_test2.bed'
adding 'pybedtools/test/data/test.fa'
adding 'pybedtools/test/data/test.fa.fai'
adding 'pybedtools/test/data/test_bedpe.bed'
adding 'pybedtools/test/data/test_peaks.bed'
adding 'pybedtools/test/data/test_tsses.bed'
adding 'pybedtools/test/data/v.vcf'
adding 'pybedtools/test/data/vcf-stderr-test.bed'
adding 'pybedtools/test/data/vcf-stderr-test.vcf'
adding 'pybedtools/test/data/venn.b.bed'
adding 'pybedtools/test/data/venn.c.bed'
adding 'pybedtools/test/data/x.bam'
adding 'pybedtools/test/data/x.bed'
adding 'pybedtools/test/data/y.bam'
adding 'pybedtools-0.10.0.dist-info/LICENSE.txt'
adding 'pybedtools-0.10.0.dist-info/METADATA'
adding 'pybedtools-0.10.0.dist-info/WHEEL'
adding 'pybedtools-0.10.0.dist-info/top_level.txt'
adding 'pybedtools-0.10.0.dist-info/RECORD'
removing build/bdist.linux-armv7l/wheel
Successfully built pybedtools-0.10.0-cp312-cp312-linux_armv7l.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module
   debian/rules execute_after_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0'
cd docs ; PYTHONPATH=/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build python3.12 -m sphinx -N -b html source html
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
[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
Matplotlib created a temporary cache directory at /tmp/matplotlib-_u1osjs9 because the default path (/nonexistent/second-build/.cache/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
[autosummary] generating autosummary for: /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.add_color.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.extend_fields.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.five_prime.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.greater_than.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.less_than.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.three_prime.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 48 source files that are out of date
updating environment: [new config] 157 added, 0 changed, 0 removed
reading sources... [  1%] 3-brief-examples
reading sources... [  1%] FAQs
reading sources... [  2%] autodoc_source
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/long_range_interaction.py.
  self[section] = content
reading sources... [  3%] autodocs/pybedtools.bedtool.BedTool
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
reading sources... [  3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance
reading sources... [  4%] autodocs/pybedtools.bedtool.BedTool.all_hits
reading sources... [  4%] autodocs/pybedtools.bedtool.BedTool.annotate
reading sources... [  5%] autodocs/pybedtools.bedtool.BedTool.any_hits
reading sources... [  6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile
reading sources... [  6%] autodocs/pybedtools.bedtool.BedTool.at
reading sources... [  7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed
reading sources... [  8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq
reading sources... [  8%] autodocs/pybedtools.bedtool.BedTool.bed6
reading sources... [  9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam
reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip
reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat
reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest
reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster
reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize
reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.complement
reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.count
reading sources... [ 14%] autodocs/pybedtools.bedtool.BedTool.count_hits
reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.coverage
reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.cut
reading sources... [ 16%] autodocs/pybedtools.bedtool.BedTool.each
reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.expand
reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.field_count
reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.file_type
reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.filter
reading sources... [ 19%] autodocs/pybedtools.bedtool.BedTool.flank
reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.genome_coverage
reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.groupby
reading sources... [ 21%] autodocs/pybedtools.bedtool.BedTool.head
reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.igv
reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.intersect
reading sources... [ 23%] autodocs/pybedtools.bedtool.BedTool.introns
reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.jaccard
reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.liftover
reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.links
reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.map
reading sources... [ 26%] autodocs/pybedtools.bedtool.BedTool.mask_fasta
reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.merge
reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.moveto
reading sources... [ 28%] autodocs/pybedtools.bedtool.BedTool.multi_bam_coverage
reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.multi_intersect
reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.nucleotide_content
reading sources... [ 30%] autodocs/pybedtools.bedtool.BedTool.overlap
reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed
reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair
reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply
reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence
reading sources... [ 33%] autodocs/pybedtools.bedtool.BedTool.random
reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard
reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op
reading sources... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection
reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection_bp
reading sources... [ 37%] autodocs/pybedtools.bedtool.BedTool.randomstats
reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.relative_distance
reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.reldist
reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.remove_invalid
reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.save_seqs
reading sources... [ 40%] autodocs/pybedtools.bedtool.BedTool.saveas
reading sources... [ 41%] autodocs/pybedtools.bedtool.BedTool.seq
reading sources... [ 41%] autodocs/pybedtools.bedtool.BedTool.sequence
reading sources... [ 42%] autodocs/pybedtools.bedtool.BedTool.set_chromsizes
reading sources... [ 43%] autodocs/pybedtools.bedtool.BedTool.shuffle
reading sources... [ 43%] autodocs/pybedtools.bedtool.BedTool.slop
reading sources... [ 44%] autodocs/pybedtools.bedtool.BedTool.sort
reading sources... [ 45%] autodocs/pybedtools.bedtool.BedTool.split
reading sources... [ 45%] autodocs/pybedtools.bedtool.BedTool.subtract
reading sources... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix
reading sources... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix_intervals
reading sources... [ 47%] autodocs/pybedtools.bedtool.BedTool.tag_bam
reading sources... [ 48%] autodocs/pybedtools.bedtool.BedTool.to_bam
reading sources... [ 48%] autodocs/pybedtools.bedtool.BedTool.total_coverage
reading sources... [ 49%] autodocs/pybedtools.bedtool.BedTool.truncate_to_chrom
reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.union_bedgraphs
reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.window
reading sources... [ 51%] autodocs/pybedtools.bedtool.BedTool.window_maker
reading sources... [ 52%] autodocs/pybedtools.bedtool.BedTool.with_attrs
reading sources... [ 52%] autodocs/pybedtools.bedtool.example_bedtool
reading sources... [ 53%] autodocs/pybedtools.cbedtools.Interval
reading sources... [ 54%] autodocs/pybedtools.cbedtools.create_interval_from_list
reading sources... [ 54%] autodocs/pybedtools.contrib.IntersectionMatrix
reading sources... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed
reading sources... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed_to_bed
reading sources... [ 56%] autodocs/pybedtools.contrib.bigwig.bam_to_bigwig
reading sources... [ 57%] autodocs/pybedtools.contrib.bigwig.bedgraph_to_bigwig
reading sources... [ 57%] autodocs/pybedtools.contrib.bigwig.wig_to_bigwig
reading sources... [ 58%] autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions
reading sources... [ 59%] autodocs/pybedtools.contrib.long_range_interaction.tag_bedpe
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/long_range_interaction.py.
  self[section] = content
reading sources... [ 59%] autodocs/pybedtools.contrib.plotting.BedToolsDemo
reading sources... [ 60%] autodocs/pybedtools.contrib.plotting.ConfiguredBedToolsDemo
reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.Track
reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.TrackCollection
reading sources... [ 62%] autodocs/pybedtools.contrib.plotting.binary_heatmap
reading sources... [ 62%] autodocs/pybedtools.contrib.plotting.binary_summary
reading sources... [ 63%] autodocs/pybedtools.contrib.venn_maker
reading sources... [ 64%] autodocs/pybedtools.contrib.venn_maker.cleaned_intersect
reading sources... [ 64%] autodocs/pybedtools.contrib.venn_maker.venn_maker
reading sources... [ 65%] autodocs/pybedtools.debug_mode
reading sources... [ 66%] autodocs/pybedtools.filenames.example_filename
reading sources... [ 66%] autodocs/pybedtools.filenames.list_example_files
reading sources... [ 67%] autodocs/pybedtools.helpers.chromsizes
reading sources... [ 68%] autodocs/pybedtools.helpers.chromsizes_to_file
reading sources... [ 68%] autodocs/pybedtools.helpers.cleanup
reading sources... [ 69%] autodocs/pybedtools.helpers.get_chromsizes_from_ucsc
reading sources... [ 69%] autodocs/pybedtools.helpers.get_tempdir
reading sources... [ 70%] autodocs/pybedtools.helpers.set_bedtools_path
reading sources... [ 71%] autodocs/pybedtools.helpers.set_tempdir
reading sources... [ 71%] autodocs/pybedtools.parallel.parallel_apply
reading sources... [ 72%] changes
reading sources... [ 73%] create-a-bedtool-tutorial
reading sources... [ 73%] default-arguments
reading sources... [ 74%] each
reading sources... [ 75%] filtering
reading sources... [ 75%] flow-of-commands
reading sources... [ 76%] history
reading sources... [ 76%] includeme
reading sources... [ 77%] index
reading sources... [ 78%] intersections
reading sources... [ 78%] intervals
reading sources... [ 79%] intro
reading sources... [ 80%] main
reading sources... [ 80%] piping
reading sources... [ 81%] pybedtools-dev-history
reading sources... [ 82%] pybedtools.featurefuncs.TSS
reading sources... [ 82%] pybedtools.featurefuncs.add_color
reading sources... [ 83%] pybedtools.featurefuncs.bed2gff
reading sources... [ 83%] pybedtools.featurefuncs.bedgraph_scale
reading sources... [ 84%] pybedtools.featurefuncs.center
reading sources... [ 85%] pybedtools.featurefuncs.extend_fields
reading sources... [ 85%] pybedtools.featurefuncs.five_prime
reading sources... [ 86%] pybedtools.featurefuncs.gff2bed
reading sources... [ 87%] pybedtools.featurefuncs.greater_than
reading sources... [ 87%] pybedtools.featurefuncs.less_than
reading sources... [ 88%] pybedtools.featurefuncs.midpoint
reading sources... [ 89%] pybedtools.featurefuncs.normalized_to_length
reading sources... [ 89%] pybedtools.featurefuncs.rename
reading sources... [ 90%] pybedtools.featurefuncs.three_prime
reading sources... [ 90%] save-results
reading sources... [ 91%] scripts
reading sources... [ 92%] sh-comparison
reading sources... [ 92%] topical-bam
reading sources... [ 93%] topical-bam-semantics
reading sources... [ 94%] topical-comparisons
reading sources... [ 94%] topical-create-a-bedtool
reading sources... [ 95%] topical-design-principles
reading sources... [ 96%] topical-documentation-contents
reading sources... [ 96%] topical-genome
reading sources... [ 97%] topical-iterators
reading sources... [ 97%] topical-low-level-ops
reading sources... [ 98%] topical-random
reading sources... [ 99%] topical-saving
reading sources... [ 99%] topical-wrapping
reading sources... [100%] tutorial-contents

WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.links' with 'bedtool.BedTool.links'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.igv' with 'bedtool.BedTool.igv'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window_maker' with 'bedtool.BedTool.window_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.groupby' with 'bedtool.BedTool.groupby'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.expand' with 'bedtool.BedTool.expand'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.each' with 'bedtool.BedTool.each'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.filter' with 'bedtool.BedTool.filter'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.split' with 'bedtool.BedTool.split'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.truncate_to_chrom' with 'bedtool.BedTool.truncate_to_chrom'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.remove_invalid' with 'bedtool.BedTool.remove_invalid'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.three_prime' with 'featurefuncs.three_prime'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.five_prime' with 'featurefuncs.five_prime'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.TSS' with 'featurefuncs.TSS'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.extend_fields' with 'featurefuncs.extend_fields'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.center' with 'featurefuncs.center'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.midpoint' with 'featurefuncs.midpoint'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.greater_than' with 'featurefuncs.greater_than'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.less_than' with 'featurefuncs.less_than'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bedgraph_scale' with 'featurefuncs.bedgraph_scale'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.add_color' with 'featurefuncs.add_color'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.gff2bed' with 'featurefuncs.gff2bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bed2gff' with 'featurefuncs.bed2gff'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.all_hits' with 'bedtool.BedTool.all_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.any_hits' with 'bedtool.BedTool.any_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count_hits' with 'bedtool.BedTool.count_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix_intervals' with 'bedtool.BedTool.tabix_intervals'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix' with 'bedtool.BedTool.tabix'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bgzip' with 'bedtool.BedTool.bgzip'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.head' with 'bedtool.BedTool.head'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count' with 'bedtool.BedTool.count'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.field_count' with 'bedtool.BedTool.field_count'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.file_type' with 'bedtool.BedTool.file_type'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.parallel_apply' with 'bedtool.BedTool.parallel_apply'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomstats' with 'bedtool.BedTool.randomstats'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection' with 'bedtool.BedTool.randomintersection'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection_bp' with 'bedtool.BedTool.randomintersection_bp'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_subset' with 'bedtool.BedTool.random_subset'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_jaccard' with 'bedtool.BedTool.random_jaccard'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_op' with 'bedtool.BedTool.random_op'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.saveas' with 'bedtool.BedTool.saveas'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.moveto' with 'bedtool.BedTool.moveto'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cat' with 'bedtool.BedTool.cat'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.at' with 'bedtool.BedTool.at'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.absolute_distance' with 'bedtool.BedTool.absolute_distance'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cut' with 'bedtool.BedTool.cut'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.total_coverage' with 'bedtool.BedTool.total_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.with_attrs' with 'bedtool.BedTool.with_attrs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.as_intervalfile' with 'bedtool.BedTool.as_intervalfile'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.introns' with 'bedtool.BedTool.introns'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.set_chromsizes' with 'bedtool.BedTool.set_chromsizes'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.print_sequence' with 'bedtool.BedTool.print_sequence'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.save_seqs' with 'bedtool.BedTool.save_seqs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.seq' with 'bedtool.BedTool.seq'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.liftover' with 'bedtool.BedTool.liftover'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.colormap_normalize' with 'bedtool.BedTool.colormap_normalize'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.relative_distance' with 'bedtool.BedTool.relative_distance'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.example_bedtool' with 'bedtool.example_bedtool'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.list_example_files' with 'filenames.list_example_files'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.example_filename' with 'filenames.example_filename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.Interval' with 'cbedtools.Interval'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.create_interval_from_list' with 'cbedtools.create_interval_from_list'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_bedtools_path' with 'helpers.set_bedtools_path'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_tempdir' with 'helpers.get_tempdir'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_tempdir' with 'helpers.set_tempdir'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.cleanup' with 'helpers.cleanup'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.debug_mode' with 'debug_mode'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_chromsizes_from_ucsc' with 'helpers.get_chromsizes_from_ucsc'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes' with 'helpers.chromsizes'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes_to_file' with 'helpers.chromsizes_to_file'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.parallel.parallel_apply' with 'parallel.parallel_apply'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.Track' with 'contrib.plotting.Track'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.TrackCollection' with 'contrib.plotting.TrackCollection'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_heatmap' with 'contrib.plotting.binary_heatmap'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_summary' with 'contrib.plotting.binary_summary'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.BedToolsDemo' with 'contrib.plotting.BedToolsDemo'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.ConfiguredBedToolsDemo' with 'contrib.plotting.ConfiguredBedToolsDemo'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bam_to_bigwig' with 'contrib.bigwig.bam_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bedgraph_to_bigwig' with 'contrib.bigwig.bedgraph_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.wig_to_bigwig' with 'contrib.bigwig.wig_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed' with 'contrib.bigbed.bigbed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed_to_bed' with 'contrib.bigbed.bigbed_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.IntersectionMatrix' with 'contrib.IntersectionMatrix'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker' with 'contrib.venn_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.venn_maker' with 'contrib.venn_maker.venn_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.cis_trans_interactions' with 'contrib.long_range_interaction.cis_trans_interactions'. [autosummary.import_cycle]
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy<https://github.com/vanheeringen-lab/genomepy/>". [docutils]
looking for now-outdated files... none found
pickling environment... done
checking consistency... /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.normalized_to_length
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename
done
preparing documents... done
copying assets... 
copying static files... 
Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/documentation_options.js
Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/language_data.js
Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/basic.css
Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/alabaster.css
copying static files: done
copying extra files... 
copying extra files: done
copying assets: done
writing output... [  1%] 3-brief-examples
writing output... [  1%] FAQs
writing output... [  2%] autodoc_source
writing output... [  3%] autodocs/pybedtools.bedtool.BedTool
writing output... [  3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance
writing output... [  4%] autodocs/pybedtools.bedtool.BedTool.all_hits
writing output... [  4%] autodocs/pybedtools.bedtool.BedTool.annotate
writing output... [  5%] autodocs/pybedtools.bedtool.BedTool.any_hits
writing output... [  6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile
writing output... [  6%] autodocs/pybedtools.bedtool.BedTool.at
writing output... [  7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed
writing output... [  8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq
writing output... [  8%] autodocs/pybedtools.bedtool.BedTool.bed6
writing output... [  9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam
writing output... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip
writing output... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat
writing output... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest
writing output... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster
writing output... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize
writing output... [ 13%] autodocs/pybedtools.bedtool.BedTool.complement
writing output... [ 13%] autodocs/pybedtools.bedtool.BedTool.count
writing output... [ 14%] autodocs/pybedtools.bedtool.BedTool.count_hits
writing output... [ 15%] autodocs/pybedtools.bedtool.BedTool.coverage
writing output... [ 15%] autodocs/pybedtools.bedtool.BedTool.cut
writing output... [ 16%] autodocs/pybedtools.bedtool.BedTool.each
writing output... [ 17%] autodocs/pybedtools.bedtool.BedTool.expand
writing output... [ 17%] autodocs/pybedtools.bedtool.BedTool.field_count
writing output... [ 18%] autodocs/pybedtools.bedtool.BedTool.file_type
writing output... [ 18%] autodocs/pybedtools.bedtool.BedTool.filter
writing output... [ 19%] autodocs/pybedtools.bedtool.BedTool.flank
writing output... [ 20%] autodocs/pybedtools.bedtool.BedTool.genome_coverage
writing output... [ 20%] autodocs/pybedtools.bedtool.BedTool.groupby
writing output... [ 21%] autodocs/pybedtools.bedtool.BedTool.head
writing output... [ 22%] autodocs/pybedtools.bedtool.BedTool.igv
writing output... [ 22%] autodocs/pybedtools.bedtool.BedTool.intersect
writing output... [ 23%] autodocs/pybedtools.bedtool.BedTool.introns
writing output... [ 24%] autodocs/pybedtools.bedtool.BedTool.jaccard
writing output... [ 24%] autodocs/pybedtools.bedtool.BedTool.liftover
writing output... [ 25%] autodocs/pybedtools.bedtool.BedTool.links
writing output... [ 25%] autodocs/pybedtools.bedtool.BedTool.map
writing output... [ 26%] autodocs/pybedtools.bedtool.BedTool.mask_fasta
writing output... [ 27%] autodocs/pybedtools.bedtool.BedTool.merge
writing output... [ 27%] autodocs/pybedtools.bedtool.BedTool.moveto
writing output... [ 28%] autodocs/pybedtools.bedtool.BedTool.multi_bam_coverage
writing output... [ 29%] autodocs/pybedtools.bedtool.BedTool.multi_intersect
writing output... [ 29%] autodocs/pybedtools.bedtool.BedTool.nucleotide_content
writing output... [ 30%] autodocs/pybedtools.bedtool.BedTool.overlap
writing output... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed
writing output... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair
writing output... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply
writing output... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence
writing output... [ 33%] autodocs/pybedtools.bedtool.BedTool.random
writing output... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard
writing output... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op
writing output... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset
writing output... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection
writing output... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection_bp
writing output... [ 37%] autodocs/pybedtools.bedtool.BedTool.randomstats
writing output... [ 38%] autodocs/pybedtools.bedtool.BedTool.relative_distance
writing output... [ 38%] autodocs/pybedtools.bedtool.BedTool.reldist
writing output... [ 39%] autodocs/pybedtools.bedtool.BedTool.remove_invalid
writing output... [ 39%] autodocs/pybedtools.bedtool.BedTool.save_seqs
writing output... [ 40%] autodocs/pybedtools.bedtool.BedTool.saveas
writing output... [ 41%] autodocs/pybedtools.bedtool.BedTool.seq
writing output... [ 41%] autodocs/pybedtools.bedtool.BedTool.sequence
writing output... [ 42%] autodocs/pybedtools.bedtool.BedTool.set_chromsizes
writing output... [ 43%] autodocs/pybedtools.bedtool.BedTool.shuffle
writing output... [ 43%] autodocs/pybedtools.bedtool.BedTool.slop
writing output... [ 44%] autodocs/pybedtools.bedtool.BedTool.sort
writing output... [ 45%] autodocs/pybedtools.bedtool.BedTool.split
writing output... [ 45%] autodocs/pybedtools.bedtool.BedTool.subtract
writing output... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix
writing output... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix_intervals
writing output... [ 47%] autodocs/pybedtools.bedtool.BedTool.tag_bam
writing output... [ 48%] autodocs/pybedtools.bedtool.BedTool.to_bam
writing output... [ 48%] autodocs/pybedtools.bedtool.BedTool.total_coverage
writing output... [ 49%] autodocs/pybedtools.bedtool.BedTool.truncate_to_chrom
writing output... [ 50%] autodocs/pybedtools.bedtool.BedTool.union_bedgraphs
writing output... [ 50%] autodocs/pybedtools.bedtool.BedTool.window
writing output... [ 51%] autodocs/pybedtools.bedtool.BedTool.window_maker
writing output... [ 52%] autodocs/pybedtools.bedtool.BedTool.with_attrs
writing output... [ 52%] autodocs/pybedtools.bedtool.example_bedtool
writing output... [ 53%] autodocs/pybedtools.cbedtools.Interval
writing output... [ 54%] autodocs/pybedtools.cbedtools.create_interval_from_list
writing output... [ 54%] autodocs/pybedtools.contrib.IntersectionMatrix
writing output... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed
writing output... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed_to_bed
writing output... [ 56%] autodocs/pybedtools.contrib.bigwig.bam_to_bigwig
writing output... [ 57%] autodocs/pybedtools.contrib.bigwig.bedgraph_to_bigwig
writing output... [ 57%] autodocs/pybedtools.contrib.bigwig.wig_to_bigwig
writing output... [ 58%] autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions
writing output... [ 59%] autodocs/pybedtools.contrib.long_range_interaction.tag_bedpe
writing output... [ 59%] autodocs/pybedtools.contrib.plotting.BedToolsDemo
writing output... [ 60%] autodocs/pybedtools.contrib.plotting.ConfiguredBedToolsDemo
writing output... [ 61%] autodocs/pybedtools.contrib.plotting.Track
writing output... [ 61%] autodocs/pybedtools.contrib.plotting.TrackCollection
writing output... [ 62%] autodocs/pybedtools.contrib.plotting.binary_heatmap
writing output... [ 62%] autodocs/pybedtools.contrib.plotting.binary_summary
writing output... [ 63%] autodocs/pybedtools.contrib.venn_maker
writing output... [ 64%] autodocs/pybedtools.contrib.venn_maker.cleaned_intersect
writing output... [ 64%] autodocs/pybedtools.contrib.venn_maker.venn_maker
writing output... [ 65%] autodocs/pybedtools.debug_mode
writing output... [ 66%] autodocs/pybedtools.filenames.example_filename
writing output... [ 66%] autodocs/pybedtools.filenames.list_example_files
writing output... [ 67%] autodocs/pybedtools.helpers.chromsizes
writing output... [ 68%] autodocs/pybedtools.helpers.chromsizes_to_file
writing output... [ 68%] autodocs/pybedtools.helpers.cleanup
writing output... [ 69%] autodocs/pybedtools.helpers.get_chromsizes_from_ucsc
writing output... [ 69%] autodocs/pybedtools.helpers.get_tempdir
writing output... [ 70%] autodocs/pybedtools.helpers.set_bedtools_path
writing output... [ 71%] autodocs/pybedtools.helpers.set_tempdir
writing output... [ 71%] autodocs/pybedtools.parallel.parallel_apply
writing output... [ 72%] changes
writing output... [ 73%] create-a-bedtool-tutorial
writing output... [ 73%] default-arguments
writing output... [ 74%] each
writing output... [ 75%] filtering
writing output... [ 75%] flow-of-commands
writing output... [ 76%] history
writing output... [ 76%] includeme
writing output... [ 77%] index
writing output... [ 78%] intersections
writing output... [ 78%] intervals
writing output... [ 79%] intro
writing output... [ 80%] main
writing output... [ 80%] piping
writing output... [ 81%] pybedtools-dev-history
writing output... [ 82%] pybedtools.featurefuncs.TSS
writing output... [ 82%] pybedtools.featurefuncs.add_color
writing output... [ 83%] pybedtools.featurefuncs.bed2gff
writing output... [ 83%] pybedtools.featurefuncs.bedgraph_scale
writing output... [ 84%] pybedtools.featurefuncs.center
writing output... [ 85%] pybedtools.featurefuncs.extend_fields
writing output... [ 85%] pybedtools.featurefuncs.five_prime
writing output... [ 86%] pybedtools.featurefuncs.gff2bed
writing output... [ 87%] pybedtools.featurefuncs.greater_than
writing output... [ 87%] pybedtools.featurefuncs.less_than
writing output... [ 88%] pybedtools.featurefuncs.midpoint
writing output... [ 89%] pybedtools.featurefuncs.normalized_to_length
writing output... [ 89%] pybedtools.featurefuncs.rename
writing output... [ 90%] pybedtools.featurefuncs.three_prime
writing output... [ 90%] save-results
writing output... [ 91%] scripts
writing output... [ 92%] sh-comparison
writing output... [ 92%] topical-bam
writing output... [ 93%] topical-bam-semantics
writing output... [ 94%] topical-comparisons
writing output... [ 94%] topical-create-a-bedtool
writing output... [ 95%] topical-design-principles
writing output... [ 96%] topical-documentation-contents
writing output... [ 96%] topical-genome
writing output... [ 97%] topical-iterators
writing output... [ 97%] topical-low-level-ops
writing output... [ 98%] topical-random
writing output... [ 99%] topical-saving
writing output... [ 99%] topical-wrapping
writing output... [100%] tutorial-contents

/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history.<locals>.decorated:9: WARNING: Lexing literal_block 'Tool:    bedtools expand \nVersion: v2.31.1\nSummary: Replicate lines in a file based on columns of comma-separated values.\n\nUsage:   bedtools expand -c [COLS] \nOptions: \n        -i      Input file. Assumes "stdin" if omitted.\n\n        -c      Specify the column (1-based) that should be summarized.\n                - Required.\nExamples: \n  $ cat test.txt\n  chr1  10      20      1,2,3   10,20,30\n  chr1  40      50      4,5,6   40,50,60\n\n  $ bedtools expand test.txt -c 5\n  chr1  10      20      1,2,3   10\n  chr1  10      20      1,2,3   20\n  chr1  10      20      1,2,3   30\n  chr1  40      50      4,5,6   40\n  chr1  40      50      4,5,6   50\n  chr1  40      50      4,5,6   60\n\n  $ bedtools expand test.txt -c 4,5\n  chr1  10      20      1       10\n  chr1  10      20      2       20\n  chr1  10      20      3       30\n  chr1  40      50      4       40\n  chr1  40      50      5       50\n  chr1  40      50      6       60' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure]
/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history.<locals>.decorated:28: WARNING: Lexing literal_block 'Tool:    bedtools groupby \nVersion: v2.31.1\nSummary: Summarizes a dataset column based upon\n         common column groupings. Akin to the SQL "group by" command.\n\nUsage:   bedtools groupby -g [group**column(s)] -c [op**column(s)] -o [ops] \n         cat [FILE] | bedtools groupby -g [group**column(s)] -c [op**column(s)] -o [ops] \n\nOptions: \n        -i              Input file. Assumes "stdin" if omitted.\n\n        -g -grp         Specify the columns (1-based) for the grouping.\n                        The columns must be comma separated.\n                        - Default: 1,2,3\n\n        -c -opCols      Specify the column (1-based) that should be summarized.\n                        - Required.\n\n        -o -ops         Specify the operation that should be applied to opCol.\n                        Valid operations:\n                            sum, count, count**distinct, min, max,\n                            mean, median, mode, antimode,\n                            stdev, sstdev (sample standard dev.),\n                            collapse (i.e., print a comma separated list (duplicates allowed)), \n                            distinct (i.e., print a comma separated list (NO duplicates allowed)), \n                            distinct**sort**num (as distinct, but sorted numerically, ascending), \n                            distinct**sort**num**desc (as distinct, but sorted numerically, descending), \n                            concat   (i.e., merge values into a single, non-delimited string), \n                            freqdesc (i.e., print desc. list of values:freq)\n                            freqasc (i.e., print asc. list of values:freq)\n                            first (i.e., print first value)\n                            last (i.e., print last value)\n                        - Default: sum\n\n                If there is only column, but multiple operations, all operations will be\n                applied on that column. Likewise, if there is only one operation, but\n                multiple columns, that operation will be applied to all columns.\n                Otherwise, the number of columns must match the the number of operations,\n                and will be applied in respective order.\n                E.g., "-c 5,4,6 -o sum,mean,count" will give the sum of column 5,\n                the mean of column 4, and the count of column 6.\n                The order of output columns will match the ordering given in the command.\n\n        -full           Print all columns from input file.  The first line in the group is used.\n                        Default: print only grouped columns.\n\n        -inheader       Input file has a header line - the first line will be ignored.\n\n        -outheader      Print header line in the output, detailing the column names. \n                        If the input file has headers (-inheader), the output file\n                        will use the input\'s column names.\n                        If the input file has no headers, the output file\n                        will use "col**1", "col**2", etc. as the column names.\n\n        -header         same as \'-inheader -outheader\'\n\n        -ignorecase     Group values regardless of upper/lower case.\n\n        -prec   Sets the decimal precision for output (Default: 5)\n\n        -delim  Specify a custom delimiter for the collapse operations.\n                - Example: -delim "|"\n                - Default: ",".\n\nExamples: \n        $ cat ex1.out\n        chr1 10  20  A   chr1    15  25  B.1 1000    ATAT\n        chr1 10  20  A   chr1    25  35  B.2 10000   CGCG\n\n        $ groupBy -i ex1.out -g 1,2,3,4 -c 9 -o sum\n        chr1 10  20  A   11000\n\n        $ groupBy -i ex1.out -grp 1,2,3,4 -opCols 9,9 -ops sum,max\n        chr1 10  20  A   11000   10000\n\n        $ groupBy -i ex1.out -g 1,2,3,4 -c 8,9 -o collapse,mean\n        chr1 10  20  A   B.1,B.2,    5500\n\n        $ cat ex1.out | groupBy -g 1,2,3,4 -c 8,9 -o collapse,mean\n        chr1 10  20  A   B.1,B.2,    5500\n\n        $ cat ex1.out | groupBy -g 1,2,3,4 -c 10 -o concat\n        chr1 10  20  A   ATATCGCG\n\nNotes: \n        (1)  The input file/stream should be sorted/grouped by the -grp. columns\n        (2)  If -i is unspecified, input is assumed to come from stdin.' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure]
/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history.<locals>.decorated:20: WARNING: Lexing literal_block 'Tool:    bedtools overlap (aka getOverlap)\nVersion: v2.31.1\nSummary: Computes the amount of overlap (positive values)\n         or distance (negative values) between genome features\n         and reports the result at the end of the same line.\n\nOptions: \n        -i      Input file. Use "stdin" for pipes.\n\n        -cols   Specify the columns (1-based) for the starts and ends of the\n                features for which you\'d like to compute the overlap/distance.\n                The columns must be listed in the following order: \n\n                start1,end1,start2,end2\n\nExample: \n        $ bedtools window -a A.bed -b B.bed -w 10\n        chr1 10  20  A   chr1    15  25  B\n        chr1 10  20  C   chr1    25  35  D\n\n        $ bedtools window -a A.bed -b B.bed -w 10 | bedtools overlap -i stdin -cols 2,3,6,7\n        chr1 10  20  A   chr1    15  25  B   5\n        chr1 10  20  C   chr1    25  35  D   -5' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure]
/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history.<locals>.decorated:16: WARNING: Lexing literal_block 'Tool: bedtools makewindows\nVersion: v2.31.1\nSummary: Makes adjacent or sliding windows across a genome or BED file.\n\nUsage: bedtools makewindows [OPTIONS] [-g <genome> OR -b <bed>]\n [ -w <window**size> OR -n <number of windows> ]\n\nInput Options: \n        -g <genome>\n                Genome file size (see notes below).\n                Windows will be created for each chromosome in the file.\n\n        -b <bed>\n                BED file (with chrom,start,end fields).\n                Windows will be created for each interval in the file.\n\nWindows Output Options: \n        -w <window**size>\n                Divide each input interval (either a chromosome or a BED interval)\n                to fixed-sized windows (i.e. same number of nucleotide in each window).\n                Can be combined with -s <step**size>\n\n        -s <step**size>\n                Step size: i.e., how many base pairs to step before\n                creating a new window. Used to create "sliding" windows.\n                - Defaults to window size (non-sliding windows).\n\n        -n <number**of**windows>\n                Divide each input interval (either a chromosome or a BED interval)\n                to fixed number of windows (i.e. same number of windows, with\n                varying window sizes).\n\n        -reverse\n                 Reverse numbering of windows in the output, i.e. report \n                 windows in decreasing order\n\nID Naming Options: \n        -i src|winnum|srcwinnum\n                The default output is 3 columns: chrom, start, end .\n                With this option, a name column will be added.\n                 "-i src" - use the source interval\'s name.\n                 "-i winnum" - use the window number as the ID (e.g. 1,2,3,4...).\n                 "-i srcwinnum" - use the source interval\'s name with the window number.\n                See below for usage examples.\n\nNotes: \n        (1) The genome file should tab delimited and structured as follows:\n         <chromName><TAB><chromSize>\n\n        For example, Human (hg19):\n        chr1    249250621\n        chr2    243199373\n        ...\n        chr18**gl000207**random 4262\n\nTip 1. Use samtools faidx to create a genome file from a FASTA: \n        One can the samtools faidx command to index a FASTA file.\n        The resulting .fai index is suitable as a genome file, \n        as bedtools will only look at the first two, relevant columns\n        of the .fai file.\n\n        For example:\n        samtools faidx GRCh38.fa\n        bedtools makewindows -w 100 -g GRCh38.fa.fai\n\nTip 2. Use UCSC Table Browser to create a genome file: \n        One can use the UCSC Genome Browser\'s MySQL database to extract\n        chromosome sizes. For example, H. sapiens:\n\n        mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\\n        "select chrom, size from hg19.chromInfo"  > hg19.genome\n\nExamples: \n # Divide the human genome into windows of 1MB:\n $ bedtools makewindows -g hg19.txt -w 1000000\n chr1 0 1000000\n chr1 1000000 2000000\n chr1 2000000 3000000\n chr1 3000000 4000000\n chr1 4000000 5000000\n ...\n\n # Divide the human genome into sliding (=overlapping) windows of 1MB, with 500KB overlap:\n $ bedtools makewindows -g hg19.txt -w 1000000 -s 500000\n chr1 0 1000000\n chr1 500000 1500000\n chr1 1000000 2000000\n chr1 1500000 2500000\n chr1 2000000 3000000\n ...\n\n # Divide each chromosome in human genome to 1000 windows of equal size:\n $ bedtools makewindows -g hg19.txt -n 1000\n chr1 0 249251\n chr1 249251 498502\n chr1 498502 747753\n chr1 747753 997004\n chr1 997004 1246255\n ...\n\n # Divide each interval in the given BED file into 10 equal-sized windows:\n $ cat input.bed\n chr5 60000 70000\n chr5 73000 90000\n chr5 100000 101000\n $ bedtools makewindows -b input.bed -n 10\n chr5 60000 61000\n chr5 61000 62000\n chr5 62000 63000\n chr5 63000 64000\n chr5 64000 65000\n ...\n\n # Add a name column, based on the window number: \n $ cat input.bed\n chr5  60000  70000 AAA\n chr5  73000  90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i winnum\n chr5        60000   63334   1\n chr5        63334   66668   2\n chr5        66668   70000   3\n chr5        73000   78667   1\n chr5        78667   84334   2\n chr5        84334   90000   3\n chr5        100000  100334  1\n chr5        100334  100668  2\n chr5        100668  101000  3\n ...\n\n # Reverse window numbers: \n $ cat input.bed\n chr5  60000  70000 AAA\n chr5  73000  90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i winnum -reverse\n chr5        60000   63334   3\n chr5        63334   66668   2\n chr5        66668   70000   1\n chr5        73000   78667   3\n chr5        78667   84334   2\n chr5        84334   90000   1\n chr5        100000  100334  3\n chr5        100334  100668  2\n chr5        100668  101000  1\n ...\n\n # Add a name column, based on the source ID + window number: \n $ cat input.bed\n chr5  60000  70000 AAA\n chr5  73000  90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i srcwinnum\n chr5        60000   63334   AAA**1\n chr5        63334   66668   AAA**2\n chr5        66668   70000   AAA**3\n chr5        73000   78667   BBB**1\n chr5        78667   84334   BBB**2\n chr5        84334   90000   BBB**3\n chr5        100000  100334  CCC**1\n chr5        100334  100668  CCC**2\n chr5        100668  101000  CCC**3\n ...' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure]
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/default-arguments.rst:35: WARNING: Lexing literal_block '$ intersectBed -a a.bed -b b.bed -u > tmpfile' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure]
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-design-principles.rst:120: WARNING: unknown option: 'mergeBed -i' [ref.option]
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-design-principles.rst:127: WARNING: unknown option: '-i' [ref.option]
generating indices... genindex py-modindex done
highlighting module code... [  8%] pybedtools
highlighting module code... [ 15%] pybedtools.bedtool
highlighting module code... [ 23%] pybedtools.cbedtools
highlighting module code... [ 31%] pybedtools.contrib.bigbed
highlighting module code... [ 38%] pybedtools.contrib.bigwig
highlighting module code... [ 46%] pybedtools.contrib.intersection_matrix
highlighting module code... [ 54%] pybedtools.contrib.long_range_interaction
highlighting module code... [ 62%] pybedtools.contrib.plotting
highlighting module code... [ 69%] pybedtools.contrib.venn_maker
highlighting module code... [ 77%] pybedtools.featurefuncs
highlighting module code... [ 85%] pybedtools.filenames
highlighting module code... [ 92%] pybedtools.helpers
highlighting module code... [100%] pybedtools.parallel

writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 133 warnings.

The HTML pages are in html.
make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0'
   dh_auto_test -O--buildsystem=pybuild
I: pybuild pybuild:308: cp /build/reproducible-path/python-pybedtools-0.10.0/debian/mpl-expected.png /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/ ;
I: pybuild base:311: cd /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build; python3.13 -m pytest -k "not test_chromsizes" --pyargs pybedtools
============================= test session starts ==============================
platform linux -- Python 3.13.1, pytest-8.3.3, pluggy-1.5.0
rootdir: /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build
configfile: pyproject.toml
plugins: typeguard-4.4.1
collected 511 items / 2 deselected / 509 selected

pybedtools/test/test_1.py .............................................. [  9%]
.......................x..x.x......                                      [ 15%]
pybedtools/test/test_cbedtools.py ...................................... [ 23%]
.                                                                        [ 23%]
pybedtools/test/test_contrib.py ..                                       [ 23%]
pybedtools/test/test_gzip_support.py ........                            [ 25%]
pybedtools/test/test_helpers.py ......                                   [ 26%]
pybedtools/test/test_issues.py ......................................... [ 34%]
..                                                                       [ 35%]
pybedtools/test/test_iter.py ........................................... [ 43%]
........................................................................ [ 57%]
........................................................................ [ 71%]
........................................................................ [ 86%]
....................................................................     [ 99%]
pybedtools/test/test_pathlib.py ...                                      [100%]

================ 506 passed, 2 deselected, 3 xfailed in 56.27s =================
I: pybuild pybuild:334: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; PYTHONPATH=/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build python3.13 -m sphinx -b doctest -d build/doctrees   source build/doctest
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, autodocs/pybedtools.bedtool.BedTool.all_hits.rst, autodocs/pybedtools.bedtool.BedTool.annotate.rst, autodocs/pybedtools.bedtool.BedTool.any_hits.rst, autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, autodocs/pybedtools.bedtool.BedTool.at.rst, autodocs/pybedtools.bedtool.BedTool.bam_to_bed.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
building [mo]: targets for 0 po files that are out of date
writing output... 
building [doctest]: targets for 157 source files that are out of date
updating environment: [new config] 157 added, 0 changed, 0 removed
reading sources... [  1%] 3-brief-examples
reading sources... [  1%] FAQs
reading sources... [  2%] autodoc_source
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/long_range_interaction.py.
  self[section] = content
reading sources... [  3%] autodocs/pybedtools.bedtool.BedTool
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
reading sources... [  3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance
reading sources... [  4%] autodocs/pybedtools.bedtool.BedTool.all_hits
reading sources... [  4%] autodocs/pybedtools.bedtool.BedTool.annotate
reading sources... [  5%] autodocs/pybedtools.bedtool.BedTool.any_hits
reading sources... [  6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile
reading sources... [  6%] autodocs/pybedtools.bedtool.BedTool.at
reading sources... [  7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed
reading sources... [  8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq
reading sources... [  8%] autodocs/pybedtools.bedtool.BedTool.bed6
reading sources... [  9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam
reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip
reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat
reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest
reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster
reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize
reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.complement
reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.count
reading sources... [ 14%] autodocs/pybedtools.bedtool.BedTool.count_hits
reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.coverage
reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.cut
reading sources... [ 16%] autodocs/pybedtools.bedtool.BedTool.each
reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.expand
reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.field_count
reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.file_type
reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.filter
reading sources... [ 19%] autodocs/pybedtools.bedtool.BedTool.flank
reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.genome_coverage
reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.groupby
reading sources... [ 21%] autodocs/pybedtools.bedtool.BedTool.head
reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.igv
reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.intersect
reading sources... [ 23%] autodocs/pybedtools.bedtool.BedTool.introns
reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.jaccard
reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.liftover
reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.links
reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.map
reading sources... [ 26%] autodocs/pybedtools.bedtool.BedTool.mask_fasta
reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.merge
reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.moveto
reading sources... [ 28%] autodocs/pybedtools.bedtool.BedTool.multi_bam_coverage
reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.multi_intersect
reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.nucleotide_content
reading sources... [ 30%] autodocs/pybedtools.bedtool.BedTool.overlap
reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed
reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair
reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply
reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence
reading sources... [ 33%] autodocs/pybedtools.bedtool.BedTool.random
reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard
reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op
reading sources... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection
reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection_bp
reading sources... [ 37%] autodocs/pybedtools.bedtool.BedTool.randomstats
reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.relative_distance
reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.reldist
reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.remove_invalid
reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.save_seqs
reading sources... [ 40%] autodocs/pybedtools.bedtool.BedTool.saveas
reading sources... [ 41%] autodocs/pybedtools.bedtool.BedTool.seq
reading sources... [ 41%] autodocs/pybedtools.bedtool.BedTool.sequence
reading sources... [ 42%] autodocs/pybedtools.bedtool.BedTool.set_chromsizes
reading sources... [ 43%] autodocs/pybedtools.bedtool.BedTool.shuffle
reading sources... [ 43%] autodocs/pybedtools.bedtool.BedTool.slop
reading sources... [ 44%] autodocs/pybedtools.bedtool.BedTool.sort
reading sources... [ 45%] autodocs/pybedtools.bedtool.BedTool.split
reading sources... [ 45%] autodocs/pybedtools.bedtool.BedTool.subtract
reading sources... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix
reading sources... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix_intervals
reading sources... [ 47%] autodocs/pybedtools.bedtool.BedTool.tag_bam
reading sources... [ 48%] autodocs/pybedtools.bedtool.BedTool.to_bam
reading sources... [ 48%] autodocs/pybedtools.bedtool.BedTool.total_coverage
reading sources... [ 49%] autodocs/pybedtools.bedtool.BedTool.truncate_to_chrom
reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.union_bedgraphs
reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.window
reading sources... [ 51%] autodocs/pybedtools.bedtool.BedTool.window_maker
reading sources... [ 52%] autodocs/pybedtools.bedtool.BedTool.with_attrs
reading sources... [ 52%] autodocs/pybedtools.bedtool.example_bedtool
reading sources... [ 53%] autodocs/pybedtools.cbedtools.Interval
reading sources... [ 54%] autodocs/pybedtools.cbedtools.create_interval_from_list
reading sources... [ 54%] autodocs/pybedtools.contrib.IntersectionMatrix
reading sources... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed
reading sources... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed_to_bed
reading sources... [ 56%] autodocs/pybedtools.contrib.bigwig.bam_to_bigwig
reading sources... [ 57%] autodocs/pybedtools.contrib.bigwig.bedgraph_to_bigwig
reading sources... [ 57%] autodocs/pybedtools.contrib.bigwig.wig_to_bigwig
reading sources... [ 58%] autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions
reading sources... [ 59%] autodocs/pybedtools.contrib.long_range_interaction.tag_bedpe
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/long_range_interaction.py.
  self[section] = content
reading sources... [ 59%] autodocs/pybedtools.contrib.plotting.BedToolsDemo
reading sources... [ 60%] autodocs/pybedtools.contrib.plotting.ConfiguredBedToolsDemo
reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.Track
reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.TrackCollection
reading sources... [ 62%] autodocs/pybedtools.contrib.plotting.binary_heatmap
reading sources... [ 62%] autodocs/pybedtools.contrib.plotting.binary_summary
reading sources... [ 63%] autodocs/pybedtools.contrib.venn_maker
reading sources... [ 64%] autodocs/pybedtools.contrib.venn_maker.cleaned_intersect
reading sources... [ 64%] autodocs/pybedtools.contrib.venn_maker.venn_maker
reading sources... [ 65%] autodocs/pybedtools.debug_mode
reading sources... [ 66%] autodocs/pybedtools.filenames.example_filename
reading sources... [ 66%] autodocs/pybedtools.filenames.list_example_files
reading sources... [ 67%] autodocs/pybedtools.helpers.chromsizes
reading sources... [ 68%] autodocs/pybedtools.helpers.chromsizes_to_file
reading sources... [ 68%] autodocs/pybedtools.helpers.cleanup
reading sources... [ 69%] autodocs/pybedtools.helpers.get_chromsizes_from_ucsc
reading sources... [ 69%] autodocs/pybedtools.helpers.get_tempdir
reading sources... [ 70%] autodocs/pybedtools.helpers.set_bedtools_path
reading sources... [ 71%] autodocs/pybedtools.helpers.set_tempdir
reading sources... [ 71%] autodocs/pybedtools.parallel.parallel_apply
reading sources... [ 72%] changes
reading sources... [ 73%] create-a-bedtool-tutorial
reading sources... [ 73%] default-arguments
reading sources... [ 74%] each
reading sources... [ 75%] filtering
reading sources... [ 75%] flow-of-commands
reading sources... [ 76%] history
reading sources... [ 76%] includeme
reading sources... [ 77%] index
reading sources... [ 78%] intersections
reading sources... [ 78%] intervals
reading sources... [ 79%] intro
reading sources... [ 80%] main
reading sources... [ 80%] piping
reading sources... [ 81%] pybedtools-dev-history
reading sources... [ 82%] pybedtools.featurefuncs.TSS
reading sources... [ 82%] pybedtools.featurefuncs.add_color
reading sources... [ 83%] pybedtools.featurefuncs.bed2gff
reading sources... [ 83%] pybedtools.featurefuncs.bedgraph_scale
reading sources... [ 84%] pybedtools.featurefuncs.center
reading sources... [ 85%] pybedtools.featurefuncs.extend_fields
reading sources... [ 85%] pybedtools.featurefuncs.five_prime
reading sources... [ 86%] pybedtools.featurefuncs.gff2bed
reading sources... [ 87%] pybedtools.featurefuncs.greater_than
reading sources... [ 87%] pybedtools.featurefuncs.less_than
reading sources... [ 88%] pybedtools.featurefuncs.midpoint
reading sources... [ 89%] pybedtools.featurefuncs.normalized_to_length
reading sources... [ 89%] pybedtools.featurefuncs.rename
reading sources... [ 90%] pybedtools.featurefuncs.three_prime
reading sources... [ 90%] save-results
reading sources... [ 91%] scripts
reading sources... [ 92%] sh-comparison
reading sources... [ 92%] topical-bam
reading sources... [ 93%] topical-bam-semantics
reading sources... [ 94%] topical-comparisons
reading sources... [ 94%] topical-create-a-bedtool
reading sources... [ 95%] topical-design-principles
reading sources... [ 96%] topical-documentation-contents
reading sources... [ 96%] topical-genome
reading sources... [ 97%] topical-iterators
reading sources... [ 97%] topical-low-level-ops
reading sources... [ 98%] topical-random
reading sources... [ 99%] topical-saving
reading sources... [ 99%] topical-wrapping
reading sources... [100%] tutorial-contents

WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.links' with 'bedtool.BedTool.links'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.igv' with 'bedtool.BedTool.igv'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window_maker' with 'bedtool.BedTool.window_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.groupby' with 'bedtool.BedTool.groupby'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.expand' with 'bedtool.BedTool.expand'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.each' with 'bedtool.BedTool.each'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.filter' with 'bedtool.BedTool.filter'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.split' with 'bedtool.BedTool.split'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.truncate_to_chrom' with 'bedtool.BedTool.truncate_to_chrom'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.remove_invalid' with 'bedtool.BedTool.remove_invalid'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.three_prime' with 'featurefuncs.three_prime'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.five_prime' with 'featurefuncs.five_prime'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.TSS' with 'featurefuncs.TSS'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.extend_fields' with 'featurefuncs.extend_fields'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.center' with 'featurefuncs.center'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.midpoint' with 'featurefuncs.midpoint'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.greater_than' with 'featurefuncs.greater_than'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.less_than' with 'featurefuncs.less_than'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bedgraph_scale' with 'featurefuncs.bedgraph_scale'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.add_color' with 'featurefuncs.add_color'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.gff2bed' with 'featurefuncs.gff2bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bed2gff' with 'featurefuncs.bed2gff'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.all_hits' with 'bedtool.BedTool.all_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.any_hits' with 'bedtool.BedTool.any_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count_hits' with 'bedtool.BedTool.count_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix_intervals' with 'bedtool.BedTool.tabix_intervals'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix' with 'bedtool.BedTool.tabix'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bgzip' with 'bedtool.BedTool.bgzip'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.head' with 'bedtool.BedTool.head'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count' with 'bedtool.BedTool.count'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.field_count' with 'bedtool.BedTool.field_count'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.file_type' with 'bedtool.BedTool.file_type'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.parallel_apply' with 'bedtool.BedTool.parallel_apply'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomstats' with 'bedtool.BedTool.randomstats'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection' with 'bedtool.BedTool.randomintersection'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection_bp' with 'bedtool.BedTool.randomintersection_bp'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_subset' with 'bedtool.BedTool.random_subset'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_jaccard' with 'bedtool.BedTool.random_jaccard'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_op' with 'bedtool.BedTool.random_op'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.saveas' with 'bedtool.BedTool.saveas'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.moveto' with 'bedtool.BedTool.moveto'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cat' with 'bedtool.BedTool.cat'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.at' with 'bedtool.BedTool.at'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.absolute_distance' with 'bedtool.BedTool.absolute_distance'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cut' with 'bedtool.BedTool.cut'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.total_coverage' with 'bedtool.BedTool.total_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.with_attrs' with 'bedtool.BedTool.with_attrs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.as_intervalfile' with 'bedtool.BedTool.as_intervalfile'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.introns' with 'bedtool.BedTool.introns'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.set_chromsizes' with 'bedtool.BedTool.set_chromsizes'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.print_sequence' with 'bedtool.BedTool.print_sequence'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.save_seqs' with 'bedtool.BedTool.save_seqs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.seq' with 'bedtool.BedTool.seq'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.liftover' with 'bedtool.BedTool.liftover'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.colormap_normalize' with 'bedtool.BedTool.colormap_normalize'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.relative_distance' with 'bedtool.BedTool.relative_distance'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.example_bedtool' with 'bedtool.example_bedtool'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.list_example_files' with 'filenames.list_example_files'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.example_filename' with 'filenames.example_filename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.Interval' with 'cbedtools.Interval'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.create_interval_from_list' with 'cbedtools.create_interval_from_list'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_bedtools_path' with 'helpers.set_bedtools_path'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_tempdir' with 'helpers.get_tempdir'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_tempdir' with 'helpers.set_tempdir'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.cleanup' with 'helpers.cleanup'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.debug_mode' with 'debug_mode'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_chromsizes_from_ucsc' with 'helpers.get_chromsizes_from_ucsc'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes' with 'helpers.chromsizes'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes_to_file' with 'helpers.chromsizes_to_file'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.parallel.parallel_apply' with 'parallel.parallel_apply'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.Track' with 'contrib.plotting.Track'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.TrackCollection' with 'contrib.plotting.TrackCollection'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_heatmap' with 'contrib.plotting.binary_heatmap'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_summary' with 'contrib.plotting.binary_summary'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.BedToolsDemo' with 'contrib.plotting.BedToolsDemo'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.ConfiguredBedToolsDemo' with 'contrib.plotting.ConfiguredBedToolsDemo'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bam_to_bigwig' with 'contrib.bigwig.bam_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bedgraph_to_bigwig' with 'contrib.bigwig.bedgraph_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.wig_to_bigwig' with 'contrib.bigwig.wig_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed' with 'contrib.bigbed.bigbed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed_to_bed' with 'contrib.bigbed.bigbed_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.IntersectionMatrix' with 'contrib.IntersectionMatrix'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker' with 'contrib.venn_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.venn_maker' with 'contrib.venn_maker.venn_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.cis_trans_interactions' with 'contrib.long_range_interaction.cis_trans_interactions'. [autosummary.import_cycle]
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy<https://github.com/vanheeringen-lab/genomepy/>". [docutils]
looking for now-outdated files... none found
pickling environment... done
checking consistency... /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.normalized_to_length
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename
done
preparing documents... done
copying assets... 
copying assets: done
running tests...

Document: autodocs/pybedtools.bedtool.BedTool.annotate
------------------------------------------------------
1 item passed all tests:
   3 tests in default
3 tests in 1 item.
3 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.cat
-------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.complement
--------------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.count
---------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.coverage
------------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.cut
-------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.each
--------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.field_count
---------------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.file_type
-------------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.filter
----------------------------------------------------
1 item passed all tests:
   3 tests in default
3 tests in 1 item.
3 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.flank
---------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.genome_coverage
-------------------------------------------------------------
1 item passed all tests:
   6 tests in default
6 tests in 1 item.
6 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.groupby
-----------------------------------------------------
1 item passed all tests:
   5 tests in default
5 tests in 1 item.
5 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.head
--------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.mask_fasta
--------------------------------------------------------
1 item passed all tests:
   8 tests in default
8 tests in 1 item.
8 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.merge
---------------------------------------------------
1 item passed all tests:
   3 tests in default
3 tests in 1 item.
3 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.moveto
----------------------------------------------------
1 item passed all tests:
   5 tests in default
5 tests in 1 item.
5 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.overlap
-----------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.random
----------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.randomintersection
----------------------------------------------------------------
1 item passed all tests:
   6 tests in default
6 tests in 1 item.
6 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.randomstats
---------------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.remove_invalid
------------------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.save_seqs
-------------------------------------------------------
1 item passed all tests:
   7 tests in default
7 tests in 1 item.
7 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.saveas
----------------------------------------------------
1 item passed all tests:
   7 tests in default
7 tests in 1 item.
7 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.sequence
------------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.set_chromsizes
------------------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.shuffle
-----------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.sort
--------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.subtract
------------------------------------------------------
1 item passed all tests:
   4 tests in default
4 tests in 1 item.
4 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.total_coverage
------------------------------------------------------------
1 item passed all tests:
   3 tests in default
3 tests in 1 item.
3 passed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.with_attrs
--------------------------------------------------------
1 item passed all tests:
   3 tests in default
3 tests in 1 item.
3 passed.
Test passed.

Document: autodocs/pybedtools.cbedtools.Interval
------------------------------------------------
1 item passed all tests:
   3 tests in default
3 tests in 1 item.
3 passed.
Test passed.

Document: autodocs/pybedtools.cbedtools.create_interval_from_list
-----------------------------------------------------------------
1 item passed all tests:
   1 test in default
1 test in 1 item.
1 passed.
Test passed.

Document: autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions
-----------------------------------------------------------------------------------
1 item passed all tests:
  18 tests in default
18 tests in 1 item.
18 passed.
Test passed.

Document: autodocs/pybedtools.contrib.plotting.Track
----------------------------------------------------
1 item passed all tests:
   7 tests in default
7 tests in 1 item.
7 passed.
Test passed.

Document: autodocs/pybedtools.filenames.list_example_files
----------------------------------------------------------
1 item passed all tests:
   5 tests in default
5 tests in 1 item.
5 passed.
Test passed.

Document: autodocs/pybedtools.helpers.chromsizes
------------------------------------------------
1 item passed all tests:
   2 tests in default
2 tests in 1 item.
2 passed.
Test passed.

Document: autodocs/pybedtools.parallel.parallel_apply
-----------------------------------------------------
1 item passed all tests:
  13 tests in default
13 tests in 1 item.
13 passed.
Test passed.

Document: default-arguments
---------------------------
1 item passed all tests:
  13 tests in default
13 tests in 1 item.
13 passed.
Test passed.

Document: each
--------------
1 item passed all tests:
   6 tests in default
6 tests in 1 item.
6 passed.
Test passed.

Document: filtering
-------------------
1 item passed all tests:
   8 tests in default
8 tests in 1 item.
8 passed.
Test passed.

Document: history
-----------------
1 item passed all tests:
  10 tests in default
10 tests in 1 item.
10 passed.
Test passed.

Document: intersections
-----------------------
1 item passed all tests:
   8 tests in default
8 tests in 1 item.
8 passed.
Test passed.

Document: intervals
-------------------
1 item passed all tests:
  50 tests in default
50 tests in 1 item.
50 passed.
Test passed.

Document: piping
----------------
1 item passed all tests:
  17 tests in default
17 tests in 1 item.
17 passed.
Test passed.

Document: save-results
----------------------
1 item passed all tests:
   8 tests in default
8 tests in 1 item.
8 passed.
Test passed.

Document: topical-bam
---------------------
1 item passed all tests:
  15 tests in default
15 tests in 1 item.
15 passed.
Test passed.

Document: topical-create-a-bedtool
----------------------------------
1 item passed all tests:
  10 tests in default
10 tests in 1 item.
10 passed.
Test passed.

Document: topical-design-principles
-----------------------------------
1 item passed all tests:
  15 tests in default
15 tests in 1 item.
15 passed.
Test passed.

Document: topical-genome
------------------------
1 item passed all tests:
  13 tests in default
13 tests in 1 item.
13 passed.
Test passed.

Document: topical-iterators
---------------------------
1 item passed all tests:
  20 tests in default
20 tests in 1 item.
20 passed.
Test passed.

Document: topical-low-level-ops
-------------------------------
1 item passed all tests:
   6 tests in default
6 tests in 1 item.
6 passed.
Test passed.

Document: topical-random
------------------------
1 item passed all tests:
  10 tests in default
10 tests in 1 item.
10 passed.
Test passed.

Document: topical-saving
------------------------
1 item passed all tests:
  14 tests in default
14 tests in 1 item.
14 passed.
Test passed.

Doctest summary
===============
  387 tests
    0 failures in tests
    0 failures in setup code
    0 failures in cleanup code
build succeeded, 126 warnings.

Testing of doctests in the sources finished, look at the results in build/doctest/output.txt.
I: pybuild pybuild:308: cp /build/reproducible-path/python-pybedtools-0.10.0/debian/mpl-expected.png /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/ ;
I: pybuild base:311: cd /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build; python3.12 -m pytest -k "not test_chromsizes" --pyargs pybedtools
============================= test session starts ==============================
platform linux -- Python 3.12.8, pytest-8.3.3, pluggy-1.5.0
rootdir: /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build
configfile: pyproject.toml
plugins: typeguard-4.4.1
collected 511 items / 2 deselected / 509 selected

pybedtools/test/test_1.py .............................................. [  9%]
.......................x..x.x......                                      [ 15%]
pybedtools/test/test_cbedtools.py ...................................... [ 23%]
.                                                                        [ 23%]
pybedtools/test/test_contrib.py ..                                       [ 23%]
pybedtools/test/test_gzip_support.py ........                            [ 25%]
pybedtools/test/test_helpers.py ......                                   [ 26%]
pybedtools/test/test_issues.py ......................................... [ 34%]
..                                                                       [ 35%]
pybedtools/test/test_iter.py ........................................... [ 43%]
........................................................................ [ 57%]
........................................................................ [ 71%]
........................................................................ [ 86%]
....................................................................     [ 99%]
pybedtools/test/test_pathlib.py ...                                      [100%]

================ 506 passed, 2 deselected, 3 xfailed in 58.03s =================
I: pybuild pybuild:334: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; PYTHONPATH=/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build python3.12 -m sphinx -b doctest -d build/doctrees   source build/doctest
Running Sphinx v8.1.3
loading translations [en]... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
loading pickled environment... failed: No module named 'pathlib._local'; 'pathlib' is not a package
done
[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, autodocs/pybedtools.bedtool.BedTool.all_hits.rst, autodocs/pybedtools.bedtool.BedTool.annotate.rst, autodocs/pybedtools.bedtool.BedTool.any_hits.rst, autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, autodocs/pybedtools.bedtool.BedTool.at.rst, autodocs/pybedtools.bedtool.BedTool.bam_to_bed.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
building [mo]: targets for 0 po files that are out of date
writing output... 
building [doctest]: targets for 157 source files that are out of date
updating environment: [new config] 157 added, 0 changed, 0 removed
reading sources... [  1%] 3-brief-examples
reading sources... [  1%] FAQs
reading sources... [  2%] autodoc_source
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/long_range_interaction.py.
  self[section] = content
reading sources... [  3%] autodocs/pybedtools.bedtool.BedTool
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
reading sources... [  3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance
reading sources... [  4%] autodocs/pybedtools.bedtool.BedTool.all_hits
reading sources... [  4%] autodocs/pybedtools.bedtool.BedTool.annotate
reading sources... [  5%] autodocs/pybedtools.bedtool.BedTool.any_hits
reading sources... [  6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile
reading sources... [  6%] autodocs/pybedtools.bedtool.BedTool.at
reading sources... [  7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed
reading sources... [  8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq
reading sources... [  8%] autodocs/pybedtools.bedtool.BedTool.bed6
reading sources... [  9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam
reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip
reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat
reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest
reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster
reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize
reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.complement
reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.count
reading sources... [ 14%] autodocs/pybedtools.bedtool.BedTool.count_hits
reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.coverage
reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.cut
reading sources... [ 16%] autodocs/pybedtools.bedtool.BedTool.each
reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.expand
reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.field_count
reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.file_type
reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.filter
reading sources... [ 19%] autodocs/pybedtools.bedtool.BedTool.flank
reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.genome_coverage
reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.groupby
reading sources... [ 21%] autodocs/pybedtools.bedtool.BedTool.head
reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.igv
reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.intersect
reading sources... [ 23%] autodocs/pybedtools.bedtool.BedTool.introns
reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.jaccard
reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.liftover
reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.links
reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.map
reading sources... [ 26%] autodocs/pybedtools.bedtool.BedTool.mask_fasta
reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.merge
reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.moveto
reading sources... [ 28%] autodocs/pybedtools.bedtool.BedTool.multi_bam_coverage
reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.multi_intersect
reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.nucleotide_content
reading sources... [ 30%] autodocs/pybedtools.bedtool.BedTool.overlap
reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed
reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair
reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply
reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence
reading sources... [ 33%] autodocs/pybedtools.bedtool.BedTool.random
reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard
reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op
reading sources... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py.
  self[section] = content
reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection
reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection_bp
reading sources... [ 37%] autodocs/pybedtools.bedtool.BedTool.randomstats
reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.relative_distance
reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.reldist
reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.remove_invalid
reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.save_seqs
reading sources... [ 40%] autodocs/pybedtools.bedtool.BedTool.saveas
reading sources... [ 41%] autodocs/pybedtools.bedtool.BedTool.seq
reading sources... [ 41%] autodocs/pybedtools.bedtool.BedTool.sequence
reading sources... [ 42%] autodocs/pybedtools.bedtool.BedTool.set_chromsizes
reading sources... [ 43%] autodocs/pybedtools.bedtool.BedTool.shuffle
reading sources... [ 43%] autodocs/pybedtools.bedtool.BedTool.slop
reading sources... [ 44%] autodocs/pybedtools.bedtool.BedTool.sort
reading sources... [ 45%] autodocs/pybedtools.bedtool.BedTool.split
reading sources... [ 45%] autodocs/pybedtools.bedtool.BedTool.subtract
reading sources... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix
reading sources... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix_intervals
reading sources... [ 47%] autodocs/pybedtools.bedtool.BedTool.tag_bam
reading sources... [ 48%] autodocs/pybedtools.bedtool.BedTool.to_bam
reading sources... [ 48%] autodocs/pybedtools.bedtool.BedTool.total_coverage
reading sources... [ 49%] autodocs/pybedtools.bedtool.BedTool.truncate_to_chrom
reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.union_bedgraphs
reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.window
reading sources... [ 51%] autodocs/pybedtools.bedtool.BedTool.window_maker
reading sources... [ 52%] autodocs/pybedtools.bedtool.BedTool.with_attrs
reading sources... [ 52%] autodocs/pybedtools.bedtool.example_bedtool
reading sources... [ 53%] autodocs/pybedtools.cbedtools.Interval
reading sources... [ 54%] autodocs/pybedtools.cbedtools.create_interval_from_list
reading sources... [ 54%] autodocs/pybedtools.contrib.IntersectionMatrix
reading sources... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed
reading sources... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed_to_bed
reading sources... [ 56%] autodocs/pybedtools.contrib.bigwig.bam_to_bigwig
reading sources... [ 57%] autodocs/pybedtools.contrib.bigwig.bedgraph_to_bigwig
reading sources... [ 57%] autodocs/pybedtools.contrib.bigwig.wig_to_bigwig
reading sources... [ 58%] autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions
reading sources... [ 59%] autodocs/pybedtools.contrib.long_range_interaction.tag_bedpe
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/long_range_interaction.py.
  self[section] = content
reading sources... [ 59%] autodocs/pybedtools.contrib.plotting.BedToolsDemo
reading sources... [ 60%] autodocs/pybedtools.contrib.plotting.ConfiguredBedToolsDemo
reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.Track
reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.TrackCollection
reading sources... [ 62%] autodocs/pybedtools.contrib.plotting.binary_heatmap
reading sources... [ 62%] autodocs/pybedtools.contrib.plotting.binary_summary
reading sources... [ 63%] autodocs/pybedtools.contrib.venn_maker
reading sources... [ 64%] autodocs/pybedtools.contrib.venn_maker.cleaned_intersect
reading sources... [ 64%] autodocs/pybedtools.contrib.venn_maker.venn_maker
reading sources... [ 65%] autodocs/pybedtools.debug_mode
reading sources... [ 66%] autodocs/pybedtools.filenames.example_filename
reading sources... [ 66%] autodocs/pybedtools.filenames.list_example_files
reading sources... [ 67%] autodocs/pybedtools.helpers.chromsizes
reading sources... [ 68%] autodocs/pybedtools.helpers.chromsizes_to_file
reading sources... [ 68%] autodocs/pybedtools.helpers.cleanup
reading sources... [ 69%] autodocs/pybedtools.helpers.get_chromsizes_from_ucsc
reading sources... [ 69%] autodocs/pybedtools.helpers.get_tempdir
reading sources... [ 70%] autodocs/pybedtools.helpers.set_bedtools_path
reading sources... [ 71%] autodocs/pybedtools.helpers.set_tempdir
reading sources... [ 71%] autodocs/pybedtools.parallel.parallel_apply
reading sources... [ 72%] changes
reading sources... [ 73%] create-a-bedtool-tutorial
reading sources... [ 73%] default-arguments
reading sources... [ 74%] each
reading sources... [ 75%] filtering
reading sources... [ 75%] flow-of-commands
reading sources... [ 76%] history
reading sources... [ 76%] includeme
reading sources... [ 77%] index
reading sources... [ 78%] intersections
reading sources... [ 78%] intervals
reading sources... [ 79%] intro
reading sources... [ 80%] main
reading sources... [ 80%] piping
reading sources... [ 81%] pybedtools-dev-history
reading sources... [ 82%] pybedtools.featurefuncs.TSS
reading sources... [ 82%] pybedtools.featurefuncs.add_color
reading sources... [ 83%] pybedtools.featurefuncs.bed2gff
reading sources... [ 83%] pybedtools.featurefuncs.bedgraph_scale
reading sources... [ 84%] pybedtools.featurefuncs.center
reading sources... [ 85%] pybedtools.featurefuncs.extend_fields
reading sources... [ 85%] pybedtools.featurefuncs.five_prime
reading sources... [ 86%] pybedtools.featurefuncs.gff2bed
reading sources... [ 87%] pybedtools.featurefuncs.greater_than
reading sources... [ 87%] pybedtools.featurefuncs.less_than
reading sources... [ 88%] pybedtools.featurefuncs.midpoint
reading sources... [ 89%] pybedtools.featurefuncs.normalized_to_length
reading sources... [ 89%] pybedtools.featurefuncs.rename
reading sources... [ 90%] pybedtools.featurefuncs.three_prime
reading sources... [ 90%] save-results
reading sources... [ 91%] scripts
reading sources... [ 92%] sh-comparison
reading sources... [ 92%] topical-bam
reading sources... [ 93%] topical-bam-semantics
reading sources... [ 94%] topical-comparisons
reading sources... [ 94%] topical-create-a-bedtool
reading sources... [ 95%] topical-design-principles
reading sources... [ 96%] topical-documentation-contents
reading sources... [ 96%] topical-genome
reading sources... [ 97%] topical-iterators
reading sources... [ 97%] topical-low-level-ops
reading sources... [ 98%] topical-random
reading sources... [ 99%] topical-saving
reading sources... [ 99%] topical-wrapping
reading sources... [100%] tutorial-contents

WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.links' with 'bedtool.BedTool.links'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.igv' with 'bedtool.BedTool.igv'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window_maker' with 'bedtool.BedTool.window_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.groupby' with 'bedtool.BedTool.groupby'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.expand' with 'bedtool.BedTool.expand'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.each' with 'bedtool.BedTool.each'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.filter' with 'bedtool.BedTool.filter'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.split' with 'bedtool.BedTool.split'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.truncate_to_chrom' with 'bedtool.BedTool.truncate_to_chrom'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.remove_invalid' with 'bedtool.BedTool.remove_invalid'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.three_prime' with 'featurefuncs.three_prime'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.five_prime' with 'featurefuncs.five_prime'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.TSS' with 'featurefuncs.TSS'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.extend_fields' with 'featurefuncs.extend_fields'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.center' with 'featurefuncs.center'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.midpoint' with 'featurefuncs.midpoint'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.greater_than' with 'featurefuncs.greater_than'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.less_than' with 'featurefuncs.less_than'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bedgraph_scale' with 'featurefuncs.bedgraph_scale'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.add_color' with 'featurefuncs.add_color'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.gff2bed' with 'featurefuncs.gff2bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bed2gff' with 'featurefuncs.bed2gff'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.all_hits' with 'bedtool.BedTool.all_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.any_hits' with 'bedtool.BedTool.any_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count_hits' with 'bedtool.BedTool.count_hits'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix_intervals' with 'bedtool.BedTool.tabix_intervals'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix' with 'bedtool.BedTool.tabix'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bgzip' with 'bedtool.BedTool.bgzip'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.head' with 'bedtool.BedTool.head'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count' with 'bedtool.BedTool.count'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.field_count' with 'bedtool.BedTool.field_count'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.file_type' with 'bedtool.BedTool.file_type'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.parallel_apply' with 'bedtool.BedTool.parallel_apply'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomstats' with 'bedtool.BedTool.randomstats'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection' with 'bedtool.BedTool.randomintersection'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection_bp' with 'bedtool.BedTool.randomintersection_bp'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_subset' with 'bedtool.BedTool.random_subset'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_jaccard' with 'bedtool.BedTool.random_jaccard'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_op' with 'bedtool.BedTool.random_op'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.saveas' with 'bedtool.BedTool.saveas'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.moveto' with 'bedtool.BedTool.moveto'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cat' with 'bedtool.BedTool.cat'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.at' with 'bedtool.BedTool.at'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.absolute_distance' with 'bedtool.BedTool.absolute_distance'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cut' with 'bedtool.BedTool.cut'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.total_coverage' with 'bedtool.BedTool.total_coverage'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.with_attrs' with 'bedtool.BedTool.with_attrs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.as_intervalfile' with 'bedtool.BedTool.as_intervalfile'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.introns' with 'bedtool.BedTool.introns'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.set_chromsizes' with 'bedtool.BedTool.set_chromsizes'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.print_sequence' with 'bedtool.BedTool.print_sequence'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.save_seqs' with 'bedtool.BedTool.save_seqs'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.seq' with 'bedtool.BedTool.seq'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.liftover' with 'bedtool.BedTool.liftover'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.colormap_normalize' with 'bedtool.BedTool.colormap_normalize'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.relative_distance' with 'bedtool.BedTool.relative_distance'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.example_bedtool' with 'bedtool.example_bedtool'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.list_example_files' with 'filenames.list_example_files'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.example_filename' with 'filenames.example_filename'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.Interval' with 'cbedtools.Interval'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.create_interval_from_list' with 'cbedtools.create_interval_from_list'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_bedtools_path' with 'helpers.set_bedtools_path'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_tempdir' with 'helpers.get_tempdir'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_tempdir' with 'helpers.set_tempdir'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.cleanup' with 'helpers.cleanup'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.debug_mode' with 'debug_mode'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_chromsizes_from_ucsc' with 'helpers.get_chromsizes_from_ucsc'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes' with 'helpers.chromsizes'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes_to_file' with 'helpers.chromsizes_to_file'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.parallel.parallel_apply' with 'parallel.parallel_apply'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.Track' with 'contrib.plotting.Track'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.TrackCollection' with 'contrib.plotting.TrackCollection'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_heatmap' with 'contrib.plotting.binary_heatmap'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_summary' with 'contrib.plotting.binary_summary'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.BedToolsDemo' with 'contrib.plotting.BedToolsDemo'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.ConfiguredBedToolsDemo' with 'contrib.plotting.ConfiguredBedToolsDemo'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bam_to_bigwig' with 'contrib.bigwig.bam_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bedgraph_to_bigwig' with 'contrib.bigwig.bedgraph_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.wig_to_bigwig' with 'contrib.bigwig.wig_to_bigwig'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed' with 'contrib.bigbed.bigbed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed_to_bed' with 'contrib.bigbed.bigbed_to_bed'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.IntersectionMatrix' with 'contrib.IntersectionMatrix'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker' with 'contrib.venn_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.venn_maker' with 'contrib.venn_maker.venn_maker'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. [autosummary.import_cycle]
WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.cis_trans_interactions' with 'contrib.long_range_interaction.cis_trans_interactions'. [autosummary.import_cycle]
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy<https://github.com/vanheeringen-lab/genomepy/>". [docutils]
looking for now-outdated files... none found
pickling environment... done
checking consistency... /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.normalized_to_length
/build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename
done
preparing documents... done
copying assets... 
copying assets: done
running tests...

Document: autodocs/pybedtools.bedtool.BedTool.annotate
------------------------------------------------------
1 items passed all tests:
   3 tests in default
3 tests in 1 items.
3 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.cat
-------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.complement
--------------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.count
---------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.coverage
------------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.cut
-------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.each
--------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.field_count
---------------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.file_type
-------------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.filter
----------------------------------------------------
1 items passed all tests:
   3 tests in default
3 tests in 1 items.
3 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.flank
---------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.genome_coverage
-------------------------------------------------------------
1 items passed all tests:
   6 tests in default
6 tests in 1 items.
6 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.groupby
-----------------------------------------------------
1 items passed all tests:
   5 tests in default
5 tests in 1 items.
5 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.head
--------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.mask_fasta
--------------------------------------------------------
1 items passed all tests:
   8 tests in default
8 tests in 1 items.
8 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.merge
---------------------------------------------------
1 items passed all tests:
   3 tests in default
3 tests in 1 items.
3 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.moveto
----------------------------------------------------
1 items passed all tests:
   5 tests in default
5 tests in 1 items.
5 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.overlap
-----------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.random
----------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.randomintersection
----------------------------------------------------------------
1 items passed all tests:
   6 tests in default
6 tests in 1 items.
6 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.randomstats
---------------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.remove_invalid
------------------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.save_seqs
-------------------------------------------------------
1 items passed all tests:
   7 tests in default
7 tests in 1 items.
7 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.saveas
----------------------------------------------------
1 items passed all tests:
   7 tests in default
7 tests in 1 items.
7 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.sequence
------------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.set_chromsizes
------------------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.shuffle
-----------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.sort
--------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.subtract
------------------------------------------------------
1 items passed all tests:
   4 tests in default
4 tests in 1 items.
4 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.total_coverage
------------------------------------------------------------
1 items passed all tests:
   3 tests in default
3 tests in 1 items.
3 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.bedtool.BedTool.with_attrs
--------------------------------------------------------
1 items passed all tests:
   3 tests in default
3 tests in 1 items.
3 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.cbedtools.Interval
------------------------------------------------
1 items passed all tests:
   3 tests in default
3 tests in 1 items.
3 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.cbedtools.create_interval_from_list
-----------------------------------------------------------------
1 items passed all tests:
   1 tests in default
1 tests in 1 items.
1 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions
-----------------------------------------------------------------------------------
1 items passed all tests:
  18 tests in default
18 tests in 1 items.
18 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.contrib.plotting.Track
----------------------------------------------------
1 items passed all tests:
   7 tests in default
7 tests in 1 items.
7 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.filenames.list_example_files
----------------------------------------------------------
1 items passed all tests:
   5 tests in default
5 tests in 1 items.
5 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.helpers.chromsizes
------------------------------------------------
1 items passed all tests:
   2 tests in default
2 tests in 1 items.
2 passed and 0 failed.
Test passed.

Document: autodocs/pybedtools.parallel.parallel_apply
-----------------------------------------------------
1 items passed all tests:
  13 tests in default
13 tests in 1 items.
13 passed and 0 failed.
Test passed.

Document: default-arguments
---------------------------
1 items passed all tests:
  13 tests in default
13 tests in 1 items.
13 passed and 0 failed.
Test passed.

Document: each
--------------
1 items passed all tests:
   6 tests in default
6 tests in 1 items.
6 passed and 0 failed.
Test passed.

Document: filtering
-------------------
1 items passed all tests:
   8 tests in default
8 tests in 1 items.
8 passed and 0 failed.
Test passed.

Document: history
-----------------
1 items passed all tests:
  10 tests in default
10 tests in 1 items.
10 passed and 0 failed.
Test passed.

Document: intersections
-----------------------
1 items passed all tests:
   8 tests in default
8 tests in 1 items.
8 passed and 0 failed.
Test passed.

Document: intervals
-------------------
1 items passed all tests:
  50 tests in default
50 tests in 1 items.
50 passed and 0 failed.
Test passed.

Document: piping
----------------
1 items passed all tests:
  17 tests in default
17 tests in 1 items.
17 passed and 0 failed.
Test passed.

Document: save-results
----------------------
1 items passed all tests:
   8 tests in default
8 tests in 1 items.
8 passed and 0 failed.
Test passed.

Document: topical-bam
---------------------
1 items passed all tests:
  15 tests in default
15 tests in 1 items.
15 passed and 0 failed.
Test passed.

Document: topical-create-a-bedtool
----------------------------------
1 items passed all tests:
  10 tests in default
10 tests in 1 items.
10 passed and 0 failed.
Test passed.

Document: topical-design-principles
-----------------------------------
1 items passed all tests:
  15 tests in default
15 tests in 1 items.
15 passed and 0 failed.
Test passed.

Document: topical-genome
------------------------
1 items passed all tests:
  13 tests in default
13 tests in 1 items.
13 passed and 0 failed.
Test passed.

Document: topical-iterators
---------------------------
1 items passed all tests:
  20 tests in default
20 tests in 1 items.
20 passed and 0 failed.
Test passed.

Document: topical-low-level-ops
-------------------------------
1 items passed all tests:
   6 tests in default
6 tests in 1 items.
6 passed and 0 failed.
Test passed.

Document: topical-random
------------------------
1 items passed all tests:
  10 tests in default
10 tests in 1 items.
10 passed and 0 failed.
Test passed.

Document: topical-saving
------------------------
1 items passed all tests:
  14 tests in default
14 tests in 1 items.
14 passed and 0 failed.
Test passed.

Doctest summary
===============
  387 tests
    0 failures in tests
    0 failures in setup code
    0 failures in cleanup code
build succeeded, 126 warnings.

Testing of doctests in the sources finished, look at the results in build/doctest/output.txt.
   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 plugin_pyproject:178: Copying package built for python3.13 to destdir
I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir
   debian/rules execute_after_dh_install
make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0'
rm -f debian/python3-pybedtools/usr/lib/python3*/dist-packages/pybedtools/test/prevent_open_file_regression \
      debian/python3-pybedtools/usr/lib/python3*/dist-packages/foo.bed \
      debian/python3-pybedtools/usr/lib/python3*/dist-packages/genome.txt
make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0'
   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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-armhf.so.3
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged
   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_0.10.0-4_all.deb'.
dpkg-deb: building package 'python-pybedtools-doc' in '../python-pybedtools-doc_0.10.0-4_all.deb'.
dpkg-deb: building package 'python3-pybedtools-dbgsym' in '../python3-pybedtools-dbgsym_0.10.0-4_armhf.deb'.
dpkg-deb: building package 'python3-pybedtools' in '../python3-pybedtools_0.10.0-4_armhf.deb'.
 dpkg-genbuildinfo --build=binary -O../python-pybedtools_0.10.0-4_armhf.buildinfo
 dpkg-genchanges --build=binary -O../python-pybedtools_0.10.0-4_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-source: info: using options from python-pybedtools-0.10.0/debian/source/options: --extend-diff-ignore=(pybedtools/version.py|docs/source/pybedtools.featurefuncs.*.rst)
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/12153/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/12153/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/12153 and its subdirectories
I: Current time: Tue Dec 31 13:28:39 +14 2024
I: pbuilder-time-stamp: 1735601319