I: pbuilder: network access will be disabled during build
I: Current time: Sat Dec 28 21:41:39 +14 2024
I: pbuilder-time-stamp: 1735371699
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
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
dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.10.0-4.dsc: unsupported subcommand
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/61238/tmp/hooks/D01_modify_environment starting
debug: Running on ionos2-i386.
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 28 07:41 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/61238/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/61238/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]="i686-pc-linux-gnu")
  BASH_VERSION='5.2.37(1)-release'
  BUILDDIR=/build/reproducible-path
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=i386
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=i686
  HOST_ARCH=i386
  IFS=' 	
  '
  INVOCATION_ID=38825571bbae428db3a2f542f30a68bc
  LANG=C
  LANGUAGE=de_CH:de
  LC_ALL=C
  LD_LIBRARY_PATH=/usr/lib/libeatmydata
  LD_PRELOAD=libeatmydata.so
  MACHTYPE=i686-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=61238
  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.gNyMwjI2/pbuilderrc_hLKk --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gNyMwjI2/b2 --logfile b2/build.log python-pybedtools_0.10.0-4.dsc'
  SUDO_GID=112
  SUDO_UID=107
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://46.16.76.132:3128
I: uname -a
  Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/61238/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), dh-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 ... 19844 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} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libidn2-0{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} libp11-kit0{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} libtasn1-6{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{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 libgpg-error-l10n 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, 246 newly installed, 0 to remove and 0 not upgraded.
Need to get 187 MB of archives. After unpacking 791 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.8-3 [816 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.8-3 [2239 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.8-1 [26.9 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024b-4 [256 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 libffi8 i386 3.4.6-1 [21.2 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB]
Get: 12 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 13 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.8-3 [1968 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.8-3 [677 kB]
Get: 22 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.8-1 [9792 B]
Get: 23 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.8-1 [27.9 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.1-2 [858 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.1-2 [2260 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-6 [876 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 openssl i386 3.3.2-2 [1387 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20241223 [164 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-3 [201 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-13 [95.9 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 ucf all 3.0046 [41.1 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 44 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-3 [723 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 bedtools i386 2.31.1+dfsg-2 [745 kB]
Get: 48 http://deb.debian.org/debian unstable/main i386 libtcl8.6 i386 8.6.15+dfsg-2 [1103 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.44-3 [288 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 53 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 54 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB]
Get: 55 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB]
Get: 59 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.10-2 [337 kB]
Get: 60 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.10-2 [834 kB]
Get: 61 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b3 [28.8 kB]
Get: 62 http://deb.debian.org/debian unstable/main i386 libxft2 i386 2.3.6-1+b3 [55.3 kB]
Get: 63 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB]
Get: 64 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB]
Get: 65 http://deb.debian.org/debian unstable/main i386 libxss1 i386 1:1.2.3-1+b2 [17.3 kB]
Get: 66 http://deb.debian.org/debian unstable/main i386 libtk8.6 i386 8.6.15-1 [833 kB]
Get: 67 http://deb.debian.org/debian unstable/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-7 [616 kB]
Get: 68 http://deb.debian.org/debian unstable/main i386 blt i386 2.5.3+dfsg-7 [6024 B]
Get: 69 http://deb.debian.org/debian unstable/main i386 cython3 i386 3.0.11+dfsg-1+b1 [3019 kB]
Get: 70 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.22 [90.5 kB]
Get: 71 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB]
Get: 72 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 73 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 74 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 75 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 76 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 77 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 78 http://deb.debian.org/debian unstable/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 79 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 80 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 81 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-3 [1631 kB]
Get: 82 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 83 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 84 http://deb.debian.org/debian unstable/main i386 debhelper all 13.22 [919 kB]
Get: 85 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 86 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get: 87 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 88 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 89 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 90 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 91 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 92 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 75.6.0-1 [222 kB]
Get: 93 http://deb.debian.org/debian unstable/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 94 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 95 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 75.6.0-1 [720 kB]
Get: 96 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20241217 [113 kB]
Get: 97 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB]
Get: 98 http://deb.debian.org/debian unstable/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 99 http://deb.debian.org/debian unstable/main i386 fontconfig i386 2.15.0-1.1+b1 [463 kB]
Get: 100 http://deb.debian.org/debian unstable/main i386 fonts-lyx all 2.4.2.1-1 [190 kB]
Get: 101 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-4 [143 kB]
Get: 102 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB]
Get: 103 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB]
Get: 104 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB]
Get: 105 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.2-2 [591 kB]
Get: 106 http://deb.debian.org/debian unstable/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB]
Get: 107 http://deb.debian.org/debian unstable/main i386 libp11-kit0 i386 0.25.5-3 [423 kB]
Get: 108 http://deb.debian.org/debian unstable/main i386 libtasn1-6 i386 4.19.0-3+b3 [51.1 kB]
Get: 109 http://deb.debian.org/debian unstable/main i386 libgnutls30t64 i386 3.8.8-2 [1451 kB]
Get: 110 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB]
Get: 111 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB]
Get: 112 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.19+dfsg-1 [200 kB]
Get: 113 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 114 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB]
Get: 115 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB]
Get: 116 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB]
Get: 117 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 118 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 119 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 120 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.11.1-1 [404 kB]
Get: 121 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.11.1-1 [393 kB]
Get: 122 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB]
Get: 123 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.22-1 [48.1 kB]
Get: 124 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.4-1 [165 kB]
Get: 125 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB]
Get: 126 http://deb.debian.org/debian unstable/main i386 libgpg-error0 i386 1.51-3 [87.3 kB]
Get: 127 http://deb.debian.org/debian unstable/main i386 libgcrypt20 i386 1.11.0-7 [799 kB]
Get: 128 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-11 [735 kB]
Get: 129 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.4-1 [1572 kB]
Get: 130 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB]
Get: 131 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 10.1.0-1 [503 kB]
Get: 132 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB]
Get: 133 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.20+ds-2 [500 kB]
Get: 134 http://deb.debian.org/debian unstable/main i386 libice6 i386 2:1.1.1-1 [67.8 kB]
Get: 135 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB]
Get: 136 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB]
Get: 137 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB]
Get: 138 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 139 http://deb.debian.org/debian unstable/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 140 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 141 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 8.1.3-3 [30.4 kB]
Get: 142 http://deb.debian.org/debian unstable/main i386 libjson-perl all 4.10000-1 [87.5 kB]
Get: 143 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-4 [2194 kB]
Get: 144 http://deb.debian.org/debian unstable/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b2 [29.5 kB]
Get: 145 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.16-2 [171 kB]
Get: 146 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB]
Get: 147 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b4 [210 kB]
Get: 148 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB]
Get: 149 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB]
Get: 150 http://deb.debian.org/debian unstable/main i386 libpango-1.0-0 i386 1.55.0+ds-3 [233 kB]
Get: 151 http://deb.debian.org/debian unstable/main i386 libpangoft2-1.0-0 i386 1.55.0+ds-3 [58.2 kB]
Get: 152 http://deb.debian.org/debian unstable/main i386 libpangocairo-1.0-0 i386 1.55.0+ds-3 [36.2 kB]
Get: 153 http://deb.debian.org/debian unstable/main i386 libpaper2 i386 2.2.5-0.3 [16.8 kB]
Get: 154 http://deb.debian.org/debian unstable/main i386 libpaper-utils i386 2.2.5-0.3 [16.1 kB]
Get: 155 http://deb.debian.org/debian unstable/main i386 libpython3.12t64 i386 3.12.8-3 [2171 kB]
Get: 156 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 157 http://deb.debian.org/debian unstable/main i386 libpython3.12-dev i386 3.12.8-3 [5296 kB]
Get: 158 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.12.8-1 [10.1 kB]
Get: 159 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.1-2 [1981 kB]
Get: 160 http://deb.debian.org/debian unstable/main i386 libpython3.13 i386 3.13.1-2 [2199 kB]
Get: 161 http://deb.debian.org/debian unstable/main i386 libpython3.13-dev i386 3.13.1-2 [5193 kB]
Get: 162 http://deb.debian.org/debian unstable/main i386 libpython3-all-dev i386 3.12.8-1 [1068 B]
Get: 163 http://deb.debian.org/debian unstable/main i386 libqhull-r8.0 i386 2020.2-6+b2 [259 kB]
Get: 164 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.2-1 [14.6 kB]
Get: 165 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB]
Get: 166 http://deb.debian.org/debian unstable/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB]
Get: 167 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB]
Get: 168 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB]
Get: 169 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.4.0-0.1+b1 [111 kB]
Get: 170 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.4.0-0.1+b1 [125 kB]
Get: 171 http://deb.debian.org/debian unstable/main i386 libxslt1.1 i386 1.1.35-1.1+b1 [243 kB]
Get: 172 http://deb.debian.org/debian unstable/main i386 libxt6t64 i386 1:1.2.1-1.2+b1 [193 kB]
Get: 173 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-2 [55.8 kB]
Get: 174 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.2-1 [55.3 kB]
Get: 175 http://deb.debian.org/debian unstable/main i386 python3-pyproject-hooks all 1.2.0-1 [11.7 kB]
Get: 176 http://deb.debian.org/debian unstable/main i386 python3-toml all 0.10.2-1 [16.2 kB]
Get: 177 http://deb.debian.org/debian unstable/main i386 python3-wheel all 0.45.1-1 [56.7 kB]
Get: 178 http://deb.debian.org/debian unstable/main i386 python3-build all 1.2.2-1 [36.0 kB]
Get: 179 http://deb.debian.org/debian unstable/main i386 python3-installer all 0.7.0+dfsg1-3 [18.6 kB]
Get: 180 http://deb.debian.org/debian unstable/main i386 pybuild-plugin-pyproject all 6.20241217 [11.5 kB]
Get: 181 http://deb.debian.org/debian unstable/main i386 python-babel-localedata all 2.16.0-1 [5696 kB]
Get: 182 http://deb.debian.org/debian unstable/main i386 python-matplotlib-data all 3.8.3-3 [2731 kB]
Get: 183 http://deb.debian.org/debian unstable/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 184 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.1-2 [740 kB]
Get: 185 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.12.8-1 [1048 B]
Get: 186 http://deb.debian.org/debian unstable/main i386 python3.12-dev i386 3.12.8-3 [505 kB]
Get: 187 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.12.8-1 [26.1 kB]
Get: 188 http://deb.debian.org/debian unstable/main i386 python3.13-dev i386 3.13.1-2 [505 kB]
Get: 189 http://deb.debian.org/debian unstable/main i386 python3-all-dev i386 3.12.8-1 [1072 B]
Get: 190 http://deb.debian.org/debian unstable/main i386 python3-attr all 24.2.0-1 [68.4 kB]
Get: 191 http://deb.debian.org/debian unstable/main i386 python3-babel all 2.16.0-1 [114 kB]
Get: 192 http://deb.debian.org/debian unstable/main i386 python3-brotli i386 1.1.0-2+b6 [319 kB]
Get: 193 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2024.8.30+dfsg-1 [9576 B]
Get: 194 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get: 195 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer i386 3.4.0-1+b1 [139 kB]
Get: 196 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-12 [4752 kB]
Get: 197 http://deb.debian.org/debian unstable/main i386 python3-contourpy i386 1.3.1-1 [271 kB]
Get: 198 http://deb.debian.org/debian unstable/main i386 python3-cycler all 0.12.1-1 [9496 B]
Get: 199 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 200 http://deb.debian.org/debian unstable/main i386 python3-decorator all 5.1.1-5 [15.1 kB]
Get: 201 http://deb.debian.org/debian unstable/main i386 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 202 http://deb.debian.org/debian unstable/main i386 python3-roman all 4.2-1 [10.4 kB]
Get: 203 http://deb.debian.org/debian unstable/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 204 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.2-1 [31.0 kB]
Get: 205 http://deb.debian.org/debian unstable/main i386 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 206 http://deb.debian.org/debian unstable/main i386 python3-fs all 2.4.16-5.1 [95.2 kB]
Get: 207 http://deb.debian.org/debian unstable/main i386 python3-lxml i386 5.3.0-1+b1 [1586 kB]
Get: 208 http://deb.debian.org/debian unstable/main i386 python3-lz4 i386 4.4.0+dfsg-1 [25.5 kB]
Get: 209 http://deb.debian.org/debian unstable/main i386 python3-scipy i386 1.14.1-3 [20.1 MB]
Get: 210 http://deb.debian.org/debian unstable/main i386 python3-mpmath all 1.3.0-1 [419 kB]
Get: 211 http://deb.debian.org/debian unstable/main i386 python3-sympy all 1.13.3-1 [4147 kB]
Get: 212 http://deb.debian.org/debian unstable/main i386 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get: 213 http://deb.debian.org/debian unstable/main i386 unicode-data all 15.1.0-1 [8547 kB]
Get: 214 http://deb.debian.org/debian unstable/main i386 python3-fonttools i386 4.55.0-3 [1593 kB]
Get: 215 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.8-2 [41.6 kB]
Get: 216 http://deb.debian.org/debian unstable/main i386 python3-imagesize all 1.4.1-1 [6688 B]
Get: 217 http://deb.debian.org/debian unstable/main i386 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 218 http://deb.debian.org/debian unstable/main i386 python3-markupsafe i386 2.1.5-1+b2 [13.9 kB]
Get: 219 http://deb.debian.org/debian unstable/main i386 python3-jinja2 all 3.1.3-1.1 [120 kB]
Get: 220 http://deb.debian.org/debian unstable/main i386 python3-kiwisolver i386 1.4.7-2+b1 [83.4 kB]
Get: 221 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.4.0-1+b1 [513 kB]
Get: 222 http://deb.debian.org/debian unstable/main i386 python3.12-tk i386 3.12.8-3 [113 kB]
Get: 223 http://deb.debian.org/debian unstable/main i386 python3.13-tk i386 3.13.1-2 [104 kB]
Get: 224 http://deb.debian.org/debian unstable/main i386 python3-tk i386 3.13.1-1 [9464 B]
Get: 225 http://deb.debian.org/debian unstable/main i386 python3-pil.imagetk i386 10.4.0-1+b1 [80.1 kB]
Get: 226 http://deb.debian.org/debian unstable/main i386 python3-pyparsing all 3.1.2-1 [146 kB]
Get: 227 http://deb.debian.org/debian unstable/main i386 python3-matplotlib i386 3.8.3-3+b1 [5660 kB]
Get: 228 http://deb.debian.org/debian unstable/main i386 sphinx-common all 8.1.3-3 [617 kB]
Get: 229 http://deb.debian.org/debian unstable/main i386 python3-pygments all 2.18.0+dfsg-1 [836 kB]
Get: 230 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 2.2.3-4 [112 kB]
Get: 231 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get: 232 http://deb.debian.org/debian unstable/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 233 http://deb.debian.org/debian unstable/main i386 python3-sphinx all 8.1.3-3 [468 kB]
Get: 234 http://deb.debian.org/debian unstable/main i386 python3-tabulate all 0.9.0-1 [45.9 kB]
Get: 235 http://deb.debian.org/debian unstable/main i386 python3-numpydoc all 1.8.0-1 [51.4 kB]
Get: 236 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.3+dfsg-5+b1 [6860 kB]
Get: 237 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.3+dfsg-5 [3096 kB]
Get: 238 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 239 http://deb.debian.org/debian unstable/main i386 python3-psutil i386 5.9.8-2 [226 kB]
Get: 240 http://deb.debian.org/debian unstable/main i386 python3-pysam i386 0.22.1+ds-2+b2 [4429 kB]
Get: 241 http://deb.debian.org/debian unstable/main i386 python3-pytest all 8.3.4-1 [250 kB]
Get: 242 http://deb.debian.org/debian unstable/main i386 python3-yaml i386 6.0.2-1+b1 [173 kB]
Get: 243 http://deb.debian.org/debian unstable/main i386 zip i386 3.0-14 [239 kB]
Get: 244 http://deb.debian.org/debian unstable/main i386 unzip i386 6.0-28 [166 kB]
Get: 245 http://deb.debian.org/debian unstable/main i386 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 246 http://deb.debian.org/debian unstable/main i386 r-base-core i386 4.4.2-1 [28.3 MB]
Fetched 187 MB in 3s (74.4 MB/s)
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Setting up libpython3.12-minimal:i386 (3.12.8-3) ...
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update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
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Processing triggers for libc-bin (2.40-4) ...
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done.
Reading package lists...
Building dependency tree...
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Initializing package states...
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 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/61238/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/61238/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 i386
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-i686-cpython-313/pybedtools
copying pybedtools/helpers.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/stats.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/paths.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/parallel.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/settings.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/version.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/logger.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/__init__.py -> build/lib.linux-i686-cpython-313/pybedtools
creating build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_issues.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_contrib.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_1.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_len_leak.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/__init__.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/regression_tests.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_helpers.py -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-i686-cpython-313/pybedtools/test
creating build/lib.linux-i686-cpython-313/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-i686-cpython-313/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-i686-cpython-313/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-i686-cpython-313/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-i686-cpython-313/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-i686-cpython-313/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-i686-cpython-313/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-i686-cpython-313/pybedtools/contrib
creating build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-i686-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-i686-cpython-313/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-i686-cpython-313/pybedtools
copying pybedtools/featurefuncs.pyx -> build/lib.linux-i686-cpython-313/pybedtools
creating build/lib.linux-i686-cpython-313/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-i686-cpython-313/pybedtools/include
copying pybedtools/include/bedFile.h -> build/lib.linux-i686-cpython-313/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-i686-cpython-313/pybedtools/include
copying pybedtools/include/fileType.h -> build/lib.linux-i686-cpython-313/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-i686-cpython-313/pybedtools/include
copying pybedtools/include/gzstream.h -> build/lib.linux-i686-cpython-313/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-i686-cpython-313/pybedtools/include
copying pybedtools/test/data/a.links.html -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test.fa -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/x.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/b.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-313/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/mpl-expected.png -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_cases.yaml -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-i686-cpython-313/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-i686-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-i686-cpython-313/pybedtools
creating build/temp.linux-i686-cpython-313/pybedtools/include
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/cbedtools.cpp -o build/temp.linux-i686-cpython-313/pybedtools/cbedtools.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/bedFile.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/fileType.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/gzstream.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/pybedtools/cbedtools.o build/temp.linux-i686-cpython-313/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-313/pybedtools/include/fileType.o build/temp.linux-i686-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o build/lib.linux-i686-cpython-313/pybedtools/cbedtools.cpython-313-i386-linux-gnu.so
building 'pybedtools.featurefuncs' extension
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/featurefuncs.cpp -o build/temp.linux-i686-cpython-313/pybedtools/featurefuncs.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/bedFile.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/fileType.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/gzstream.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/pybedtools/featurefuncs.o build/temp.linux-i686-cpython-313/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-313/pybedtools/include/fileType.o build/temp.linux-i686-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o build/lib.linux-i686-cpython-313/pybedtools/featurefuncs.cpython-313-i386-linux-gnu.so
installing to build/bdist.linux-i686/wheel
running install
running install_lib
creating build/bdist.linux-i686/wheel
creating build/bdist.linux-i686/wheel/pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/featurefuncs.cpython-313-i386-linux-gnu.so -> build/bdist.linux-i686/wheel/./pybedtools
creating build/bdist.linux-i686/wheel/pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_merge227.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_issues.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
creating build/bdist.linux-i686/wheel/pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/a.links.html -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/small.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/test.fa -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/v.vcf -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/venn.c.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/y.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/bedpe.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/a.igv_script -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/164.gtf -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/venn.b.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/hg19.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/x.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/x.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/reads.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/issue_121.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/genome.fa -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.cram -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/issue319.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/small.fastq -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/__init__.py -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/m1.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/expand_test.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/exons.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/test.fa.fai -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/d.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/c.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/b.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/a.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-313/pybedtools/test/genomepy_integration.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_merge215.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_cbedtools.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_contrib.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_iter.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/gchart-expected.png -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_gzip_support.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/mpl-expected.png -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_1.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_len_leak.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_cases.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/__init__.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/regression_tests.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/tfuncs.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_helpers.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/test/test_pathlib.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-313/pybedtools/featurefuncs.pyx -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/helpers.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/stats.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/paths.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/bedtool.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/parallel.py -> build/bdist.linux-i686/wheel/./pybedtools
creating build/bdist.linux-i686/wheel/pybedtools/contrib
copying build/lib.linux-i686-cpython-313/pybedtools/contrib/venn_maker.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-313/pybedtools/contrib/bigwig.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-313/pybedtools/contrib/bigbed.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-313/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-313/pybedtools/contrib/plotting.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-313/pybedtools/contrib/__init__.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-313/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-313/pybedtools/filenames.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/settings.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/_Window.pyx -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/version.py -> build/bdist.linux-i686/wheel/./pybedtools
creating build/bdist.linux-i686/wheel/pybedtools/include
copying build/lib.linux-i686-cpython-313/pybedtools/include/fileType.cpp -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-313/pybedtools/include/bedFile.cpp -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-313/pybedtools/include/gzstream.cpp -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-313/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-313/pybedtools/include/bedFile.h -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-313/pybedtools/include/fileType.h -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-313/pybedtools/include/gzstream.h -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-313/pybedtools/logger.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/cbedtools.cpython-313-i386-linux-gnu.so -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/genome_registry.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/cbedtools.pxd -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/cbedtools.pyx -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-313/pybedtools/__init__.py -> build/bdist.linux-i686/wheel/./pybedtools
running install_egg_info
Copying pybedtools.egg-info to build/bdist.linux-i686/wheel/./pybedtools-0.10.0.egg-info
running install_scripts
creating build/bdist.linux-i686/wheel/pybedtools-0.10.0.dist-info/WHEEL
creating '/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/.tmp-ntyvvz3d/pybedtools-0.10.0-cp313-cp313-linux_i686.whl' and adding 'build/bdist.linux-i686/wheel' to it
adding 'pybedtools/_Window.pyx'
adding 'pybedtools/__init__.py'
adding 'pybedtools/bedtool.py'
adding 'pybedtools/cbedtools.cpython-313-i386-linux-gnu.so'
adding 'pybedtools/cbedtools.pxd'
adding 'pybedtools/cbedtools.pyx'
adding 'pybedtools/featurefuncs.cpython-313-i386-linux-gnu.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-i686/wheel
Successfully built pybedtools-0.10.0-cp313-cp313-linux_i686.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-i686-cpython-312/pybedtools
copying pybedtools/helpers.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/stats.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/paths.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/parallel.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/settings.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/version.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/logger.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/__init__.py -> build/lib.linux-i686-cpython-312/pybedtools
creating build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_issues.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_contrib.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_1.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_len_leak.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/__init__.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/regression_tests.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_helpers.py -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-i686-cpython-312/pybedtools/test
creating build/lib.linux-i686-cpython-312/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib
creating build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-i686-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-i686-cpython-312/pybedtools
copying pybedtools/cbedtools.cpp -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/featurefuncs.cpp -> build/lib.linux-i686-cpython-312/pybedtools
copying pybedtools/featurefuncs.pyx -> build/lib.linux-i686-cpython-312/pybedtools
creating build/lib.linux-i686-cpython-312/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-i686-cpython-312/pybedtools/include
copying pybedtools/include/bedFile.h -> build/lib.linux-i686-cpython-312/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-i686-cpython-312/pybedtools/include
copying pybedtools/include/fileType.h -> build/lib.linux-i686-cpython-312/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-i686-cpython-312/pybedtools/include
copying pybedtools/include/gzstream.h -> build/lib.linux-i686-cpython-312/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-i686-cpython-312/pybedtools/include
copying pybedtools/test/data/a.links.html -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test.fa -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/x.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/b.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/mpl-expected.png -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_cases.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
creating build/temp.linux-i686-cpython-312/pybedtools
creating build/temp.linux-i686-cpython-312/pybedtools/include
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-i686-cpython-312/pybedtools/cbedtools.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/pybedtools/cbedtools.o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o build/lib.linux-i686-cpython-312/pybedtools/cbedtools.cpython-312-i386-linux-gnu.so
building 'pybedtools.featurefuncs' extension
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-i686-cpython-312/pybedtools/featurefuncs.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o
i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/pybedtools/featurefuncs.o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o build/lib.linux-i686-cpython-312/pybedtools/featurefuncs.cpython-312-i386-linux-gnu.so
installing to build/bdist.linux-i686/wheel
running install
running install_lib
creating build/bdist.linux-i686/wheel
creating build/bdist.linux-i686/wheel/pybedtools
creating build/bdist.linux-i686/wheel/pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_merge227.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_issues.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
creating build/bdist.linux-i686/wheel/pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/a.links.html -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/small.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test.fa -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/v.vcf -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/venn.c.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/y.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/bedpe.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/a.igv_script -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/164.gtf -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/venn.b.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/hg19.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/x.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/x.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/reads.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/issue_121.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/genome.fa -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.cram -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/issue319.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/small.fastq -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/__init__.py -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/m1.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/expand_test.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/exons.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test.fa.fai -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/d.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/c.gff -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/b.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/a.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/wheel/./pybedtools/test/data
copying build/lib.linux-i686-cpython-312/pybedtools/test/genomepy_integration.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_merge215.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_cbedtools.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_contrib.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_iter.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/gchart-expected.png -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_gzip_support.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/mpl-expected.png -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_1.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_len_leak.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_cases.yaml -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/__init__.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/regression_tests.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/tfuncs.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_helpers.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/test/test_pathlib.py -> build/bdist.linux-i686/wheel/./pybedtools/test
copying build/lib.linux-i686-cpython-312/pybedtools/featurefuncs.pyx -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/helpers.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/stats.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/paths.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/bedtool.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/parallel.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/featurefuncs.cpython-312-i386-linux-gnu.so -> build/bdist.linux-i686/wheel/./pybedtools
creating build/bdist.linux-i686/wheel/pybedtools/contrib
copying build/lib.linux-i686-cpython-312/pybedtools/contrib/venn_maker.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-312/pybedtools/contrib/bigwig.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-312/pybedtools/contrib/bigbed.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-312/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-312/pybedtools/contrib/plotting.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-312/pybedtools/contrib/__init__.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-312/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-i686/wheel/./pybedtools/contrib
copying build/lib.linux-i686-cpython-312/pybedtools/filenames.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/settings.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/_Window.pyx -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/version.py -> build/bdist.linux-i686/wheel/./pybedtools
creating build/bdist.linux-i686/wheel/pybedtools/include
copying build/lib.linux-i686-cpython-312/pybedtools/include/fileType.cpp -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-312/pybedtools/include/bedFile.cpp -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-312/pybedtools/include/gzstream.cpp -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-312/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-312/pybedtools/include/bedFile.h -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-312/pybedtools/include/fileType.h -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-312/pybedtools/include/gzstream.h -> build/bdist.linux-i686/wheel/./pybedtools/include
copying build/lib.linux-i686-cpython-312/pybedtools/logger.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/genome_registry.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/cbedtools.pxd -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/cbedtools.pyx -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/cbedtools.cpp -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/__init__.py -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/featurefuncs.cpp -> build/bdist.linux-i686/wheel/./pybedtools
copying build/lib.linux-i686-cpython-312/pybedtools/cbedtools.cpython-312-i386-linux-gnu.so -> build/bdist.linux-i686/wheel/./pybedtools
running install_egg_info
Copying pybedtools.egg-info to build/bdist.linux-i686/wheel/./pybedtools-0.10.0.egg-info
running install_scripts
creating build/bdist.linux-i686/wheel/pybedtools-0.10.0.dist-info/WHEEL
creating '/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/.tmp-__hm4roi/pybedtools-0.10.0-cp312-cp312-linux_i686.whl' and adding 'build/bdist.linux-i686/wheel' to it
adding 'pybedtools/_Window.pyx'
adding 'pybedtools/__init__.py'
adding 'pybedtools/bedtool.py'
adding 'pybedtools/cbedtools.cpp'
adding 'pybedtools/cbedtools.cpython-312-i386-linux-gnu.so'
adding 'pybedtools/cbedtools.pxd'
adding 'pybedtools/cbedtools.pyx'
adding 'pybedtools/featurefuncs.cpp'
adding 'pybedtools/featurefuncs.cpython-312-i386-linux-gnu.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-i686/wheel
Successfully built pybedtools-0.10.0-cp312-cp312-linux_i686.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-gc844zp0 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
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  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.
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/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.
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/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.
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reading sources... [ 93%] topical-bam-semantics
reading sources... [ 94%] topical-comparisons
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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]
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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]
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WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.each' with 'bedtool.BedTool.each'. [autosummary.import_cycle]
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/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]
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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
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/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]
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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 ==============================
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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
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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
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reading sources... [ 73%] default-arguments
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reading sources... [ 76%] includeme
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reading sources... [ 78%] intersections
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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
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reading sources... [ 84%] pybedtools.featurefuncs.center
reading sources... [ 85%] pybedtools.featurefuncs.extend_fields
reading sources... [ 85%] pybedtools.featurefuncs.five_prime
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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]
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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]
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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]
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WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection' with 'bedtool.BedTool.randomintersection'. [autosummary.import_cycle]
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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]
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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]
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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]
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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]
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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]
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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]
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/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
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running tests...

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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-8.3.4, 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%]
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pybedtools/test/test_pathlib.py ...                                      [100%]

================ 506 passed, 2 deselected, 3 xfailed in 36.86s =================
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
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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

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/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
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Document: autodocs/pybedtools.bedtool.BedTool.cat
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Document: autodocs/pybedtools.bedtool.BedTool.field_count
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Document: autodocs/pybedtools.bedtool.BedTool.flank
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Document: autodocs/pybedtools.bedtool.BedTool.genome_coverage
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Document: autodocs/pybedtools.bedtool.BedTool.mask_fasta
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Document: autodocs/pybedtools.bedtool.BedTool.merge
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Document: autodocs/pybedtools.bedtool.BedTool.moveto
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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.
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