I: pbuilder: network access will be disabled during build
I: Current time: Sat Feb 22 17:13:01 +14 2025
I: pbuilder-time-stamp: 1740193981
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [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/1448169/tmp/hooks/D01_modify_environment starting
debug: Running on ionos11-amd64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Feb 22 03:13 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/1448169/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/1448169/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]="x86_64-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=amd64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=x86_64
  HOST_ARCH=amd64
  IFS=' 	
  '
  INVOCATION_ID=7dc5a94ee8f045b28ffcccef101e7974
  LANG=C
  LANGUAGE=et_EE:et
  LC_ALL=C
  MACHTYPE=x86_64-pc-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=1448169
  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.33QFcy8h/pbuilderrc_5ORz --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.33QFcy8h/b2 --logfile b2/build.log python-pybedtools_0.10.0-4.dsc'
  SUDO_GID=111
  SUDO_UID=106
  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 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) 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/1448169/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <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 ... 19775 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} libldap2{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} libtext-charwidth-perl{a} libtext-wrapi18n-perl{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-numpy-dev{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-pytz{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-numba 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, 250 newly installed, 0 to remove and 0 not upgraded.
Need to get 191 MB of archives. After unpacking 808 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 11.0.0 [27.6 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025a-2 [259 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-1 [1979 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-1 [745 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B]
Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.3+ds-2 [138 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-2 [160 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-17 [836 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-2 [2452 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.3+ds-2 [7517 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.9-1 [817 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.9-1 [2163 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.4.1-1 [1427 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-4 [92.4 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 39 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0050 [42.7 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.16+dfsg-1 [1042 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1 [282 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2 [317 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2 [391 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b4 [27.8 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b4 [54.5 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b3 [17.0 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.16-1 [793 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B]
Get: 67 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2 [3159 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 74 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.6.0-1 [65.3 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.8.0-1 [222 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.8.0-1 [724 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-2 [463 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.3-1 [190 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-2 [365 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.12.1-2 [369 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB]
Get: 128 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get: 131 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.83.4-1 [1512 kB]
Get: 132 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1 [479 kB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 143 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB]
Get: 144 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 145 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB]
Get: 146 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 147 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 148 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 149 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB]
Get: 150 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB]
Get: 151 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-1 [204 kB]
Get: 152 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 153 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get: 154 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.56.1-1 [226 kB]
Get: 155 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.56.1-1 [55.3 kB]
Get: 156 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.56.1-1 [35.8 kB]
Get: 157 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB]
Get: 158 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB]
Get: 159 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.2-1 [2151 kB]
Get: 160 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 161 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.2-1 [5005 kB]
Get: 162 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.1-2 [10.2 kB]
Get: 163 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.9-1 [1974 kB]
Get: 164 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.9-1 [2151 kB]
Get: 165 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.9-1 [5125 kB]
Get: 166 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.1-2 [1072 B]
Get: 167 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB]
Get: 168 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB]
Get: 169 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 170 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB]
Get: 171 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 172 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB]
Get: 173 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB]
Get: 174 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB]
Get: 175 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB]
Get: 176 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB]
Get: 177 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB]
Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 179 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB]
Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-toml all 0.10.2-1 [16.2 kB]
Get: 181 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.45.1-1 [56.7 kB]
Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-1 [36.0 kB]
Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB]
Get: 184 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250108 [11.6 kB]
Get: 185 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.17.0-1 [6050 kB]
Get: 186 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB]
Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get: 188 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.9-1 [681 kB]
Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.1-2 [1056 B]
Get: 190 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.2-1 [507 kB]
Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.1-2 [26.1 kB]
Get: 192 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.9-1 [505 kB]
Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.1-2 [1076 B]
Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-attr all 25.1.0-1 [68.7 kB]
Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.17.0-1 [117 kB]
Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB]
Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2025.1.31+ds-1 [9652 B]
Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-2 [108 kB]
Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.1-1 [142 kB]
Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB]
Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B]
Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB]
Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB]
Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-roman all 5.0-1 [10.6 kB]
Get: 206 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-pytz all 2025.1-3 [150 kB]
Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2025.1-3 [4004 B]
Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB]
Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-6 [95.1 kB]
Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.1-1 [1683 kB]
Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB]
Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.14.1-4 [20.5 MB]
Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB]
Get: 215 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.13.3-3 [4148 kB]
Get: 216 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB]
Get: 217 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB]
Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.55.3-2 [1633 kB]
Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.10-1 [42.0 kB]
Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B]
Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B]
Get: 222 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB]
Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.5-2 [107 kB]
Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-3 [76.9 kB]
Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 11.1.0-5 [531 kB]
Get: 226 http://deb.debian.org/debian unstable/main amd64 python3.12-tk amd64 3.12.9-1 [113 kB]
Get: 227 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.2-1 [103 kB]
Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.1-1 [9464 B]
Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 11.1.0-5 [81.5 kB]
Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB]
Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.8.3-3+b3 [5650 kB]
Get: 232 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-5 [617 kB]
Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB]
Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.3.0-1 [114 kB]
Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-4 [72.1 kB]
Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get: 237 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-5 [468 kB]
Get: 238 http://deb.debian.org/debian unstable/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB]
Get: 239 http://deb.debian.org/debian unstable/main amd64 python3-numpydoc all 1.8.0-1 [51.4 kB]
Get: 240 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-8 [7295 kB]
Get: 241 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-8 [3097 kB]
Get: 242 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get: 243 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 5.9.8-2 [225 kB]
Get: 244 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.23.0+ds-1 [4527 kB]
Get: 245 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB]
Get: 246 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB]
Get: 247 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB]
Get: 248 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 249 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 250 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB]
Fetched 191 MB in 10s (19.1 MB/s)
Preconfiguring packages ...
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Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ...
Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ...
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Current default time zone: 'Etc/UTC'
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Creating config file /etc/R/Renviron with new version
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done.
Reading package lists...
Building dependency tree...
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Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/1448169/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/1448169/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 amd64
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 python3.12 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:270: 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:124: 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-x86_64-cpython-312/pybedtools
copying pybedtools/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/parallel.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/paths.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/version.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/logger.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/helpers.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-x86_64-cpython-312/pybedtools
creating build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_1.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_issues.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test
creating build/lib.linux-x86_64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib
creating build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-cpython-312/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-x86_64-cpython-312/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-x86_64-cpython-312/pybedtools
copying pybedtools/featurefuncs.pyx -> build/lib.linux-x86_64-cpython-312/pybedtools
creating build/lib.linux-x86_64-cpython-312/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-x86_64-cpython-312/pybedtools/include
copying pybedtools/include/bedFile.h -> build/lib.linux-x86_64-cpython-312/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-x86_64-cpython-312/pybedtools/include
copying pybedtools/include/fileType.h -> build/lib.linux-x86_64-cpython-312/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-x86_64-cpython-312/pybedtools/include
copying pybedtools/include/gzstream.h -> build/lib.linux-x86_64-cpython-312/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-x86_64-cpython-312/pybedtools/include
copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/mpl-expected.png -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_cases.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-x86_64-cpython-312/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-x86_64-cpython-312/pybedtools
creating build/temp.linux-x86_64-cpython-312/pybedtools/include
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/cbedtools.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so
building 'pybedtools.featurefuncs' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/featurefuncs.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o build/lib.linux-x86_64-cpython-312/pybedtools/featurefuncs.cpython-312-x86_64-linux-gnu.so
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/stats.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/genome_registry.py -> build/bdist.linux-x86_64/wheel/./pybedtools
creating build/bdist.linux-x86_64/wheel/pybedtools/include
copying build/lib.linux-x86_64-cpython-312/pybedtools/include/gzstream.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-312/pybedtools/include/fileType.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-312/pybedtools/include/bedFile.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-312/pybedtools/include/gzstream.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-312/pybedtools/include/fileType.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-312/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-312/pybedtools/include/bedFile.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/parallel.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/filenames.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/paths.py -> build/bdist.linux-x86_64/wheel/./pybedtools
creating build/bdist.linux-x86_64/wheel/pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_cbedtools.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/genomepy_integration.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_1.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_len_leak.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_contrib.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/regression_tests.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/mpl-expected.png -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_gzip_support.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/gchart-expected.png -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_cases.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/tfuncs.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_merge215.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
creating build/bdist.linux-x86_64/wheel/pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/b.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/d.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test.fa.fai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/issue_121.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test.fa -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/venn.b.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/a.links.html -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/a.igv_script -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/venn.c.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.cram -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/exons.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/y.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/small.fastq -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/small.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/c.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/reads.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/v.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/x.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/hg19.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/genome.fa -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/issue319.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/m1.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/x.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/164.gtf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/a.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/bedpe.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/expand_test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_pathlib.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_merge227.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_helpers.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_iter.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_issues.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-312/pybedtools/version.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/logger.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.pxd -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/featurefuncs.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/helpers.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/settings.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/featurefuncs.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/bedtool.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-312/pybedtools/_Window.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools
creating build/bdist.linux-x86_64/wheel/pybedtools/contrib
copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/bigwig.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/venn_maker.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/bigbed.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/plotting.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
running install_egg_info
Copying pybedtools.egg-info to build/bdist.linux-x86_64/wheel/./pybedtools-0.10.0.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/pybedtools-0.10.0.dist-info/WHEEL
creating '/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/.tmp-vf48udai/pybedtools-0.10.0-cp312-cp312-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'pybedtools/_Window.pyx'
adding 'pybedtools/__init__.py'
adding 'pybedtools/bedtool.py'
adding 'pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so'
adding 'pybedtools/cbedtools.pxd'
adding 'pybedtools/cbedtools.pyx'
adding 'pybedtools/featurefuncs.cpython-312-x86_64-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-x86_64/wheel
Successfully built pybedtools-0.10.0-cp312-cp312-linux_x86_64.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module
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:270: 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:124: 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-x86_64-cpython-313/pybedtools
copying pybedtools/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/parallel.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/paths.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/version.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/logger.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/helpers.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-x86_64-cpython-313/pybedtools
creating build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_1.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_issues.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test
creating build/lib.linux-x86_64-cpython-313/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib
creating build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-cpython-313/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-x86_64-cpython-313/pybedtools
copying pybedtools/cbedtools.cpp -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/featurefuncs.cpp -> build/lib.linux-x86_64-cpython-313/pybedtools
copying pybedtools/featurefuncs.pyx -> build/lib.linux-x86_64-cpython-313/pybedtools
creating build/lib.linux-x86_64-cpython-313/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-x86_64-cpython-313/pybedtools/include
copying pybedtools/include/bedFile.h -> build/lib.linux-x86_64-cpython-313/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-x86_64-cpython-313/pybedtools/include
copying pybedtools/include/fileType.h -> build/lib.linux-x86_64-cpython-313/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-x86_64-cpython-313/pybedtools/include
copying pybedtools/include/gzstream.h -> build/lib.linux-x86_64-cpython-313/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-x86_64-cpython-313/pybedtools/include
copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/mpl-expected.png -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_cases.yaml -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-x86_64-cpython-313/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-x86_64-cpython-313/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
creating build/temp.linux-x86_64-cpython-313/pybedtools
creating build/temp.linux-x86_64-cpython-313/pybedtools/include
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/cbedtools.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/bedFile.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/fileType.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/gzstream.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-313/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-313/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.cpython-313-x86_64-linux-gnu.so
building 'pybedtools.featurefuncs' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/featurefuncs.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/featurefuncs.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/bedFile.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/fileType.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/gzstream.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-313/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-313/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o build/lib.linux-x86_64-cpython-313/pybedtools/featurefuncs.cpython-313-x86_64-linux-gnu.so
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/stats.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/genome_registry.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools
creating build/bdist.linux-x86_64/wheel/pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/include/gzstream.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/include/fileType.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/include/bedFile.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/include/gzstream.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/include/fileType.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/include/bedFile.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/featurefuncs.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/parallel.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/filenames.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/paths.py -> build/bdist.linux-x86_64/wheel/./pybedtools
creating build/bdist.linux-x86_64/wheel/pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_cbedtools.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/genomepy_integration.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_1.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_len_leak.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_contrib.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/regression_tests.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/mpl-expected.png -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_gzip_support.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/gchart-expected.png -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_cases.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/tfuncs.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_merge215.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
creating build/bdist.linux-x86_64/wheel/pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/b.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/d.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test.fa.fai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue_121.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test.fa -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/venn.b.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/a.links.html -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/a.igv_script -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/venn.c.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.cram -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/exons.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/y.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/small.fastq -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/small.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/c.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/reads.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/v.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/x.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/hg19.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/genome.fa -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue319.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/m1.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/x.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/164.gtf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/a.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/bedpe.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/expand_test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_pathlib.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_merge227.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_helpers.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_iter.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_issues.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-x86_64/wheel/./pybedtools/test
copying build/lib.linux-x86_64-cpython-313/pybedtools/featurefuncs.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/version.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/logger.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.pxd -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/featurefuncs.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/helpers.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/settings.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/bedtool.py -> build/bdist.linux-x86_64/wheel/./pybedtools
copying build/lib.linux-x86_64-cpython-313/pybedtools/_Window.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools
creating build/bdist.linux-x86_64/wheel/pybedtools/contrib
copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/bigwig.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/venn_maker.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/bigbed.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/plotting.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib
running install_egg_info
Copying pybedtools.egg-info to build/bdist.linux-x86_64/wheel/./pybedtools-0.10.0.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/pybedtools-0.10.0.dist-info/WHEEL
creating '/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/.tmp-iwshhzyp/pybedtools-0.10.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'pybedtools/_Window.pyx'
adding 'pybedtools/__init__.py'
adding 'pybedtools/bedtool.py'
adding 'pybedtools/cbedtools.cpp'
adding 'pybedtools/cbedtools.cpython-313-x86_64-linux-gnu.so'
adding 'pybedtools/cbedtools.pxd'
adding 'pybedtools/cbedtools.pyx'
adding 'pybedtools/featurefuncs.cpp'
adding 'pybedtools/featurefuncs.cpython-313-x86_64-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-x86_64/wheel
Successfully built pybedtools-0.10.0-cp313-cp313-linux_x86_64.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 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_3.13_pybedtools/build python3.13 -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-h3uj9geu 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
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building [html]: targets for 48 source files that are out of date
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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_3.13_pybedtools/build/pybedtools/contrib/long_range_interaction.py.
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reading sources... [ 95%] topical-design-principles
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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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/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_3.13_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_3.13_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_3.13_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_3.13_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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make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0'
   dh_auto_test -O--buildsystem=pybuild
I: pybuild pybuild:308: cp /build/reproducible-path/python-pybedtools-0.10.0/debian/mpl-expected.png /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_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 3.12.9, 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
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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_3.12_pybedtools/build python3.12 -m sphinx -b doctest -d build/doctrees   source build/doctest
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, autodocs/pybedtools.bedtool.BedTool.all_hits.rst, autodocs/pybedtools.bedtool.BedTool.annotate.rst, autodocs/pybedtools.bedtool.BedTool.any_hits.rst, autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, autodocs/pybedtools.bedtool.BedTool.at.rst, autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst
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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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/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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/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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Doctest summary
===============
  387 tests
    0 failures in tests
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    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_3.13_pybedtools/build/pybedtools/test/ ;
I: pybuild base:311: cd /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build; python3.13 -m pytest -k "not test_chromsizes" --pyargs pybedtools
============================= test session starts ==============================
platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0
rootdir: /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build
configfile: pyproject.toml
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pybedtools/test/test_1.py .............................................. [  9%]
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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 131.80s (0:02:11) ===========
I: pybuild pybuild:334: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; PYTHONPATH=/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build python3.13 -m sphinx -b doctest -d build/doctrees   source build/doctest
Running Sphinx v8.1.3
loading translations [en]... done
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[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, autodocs/pybedtools.bedtool.BedTool.all_hits.rst, autodocs/pybedtools.bedtool.BedTool.annotate.rst, autodocs/pybedtools.bedtool.BedTool.any_hits.rst, autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, autodocs/pybedtools.bedtool.BedTool.at.rst, autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst
building [mo]: targets for 0 po files that are out of date
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updating environment: 0 added, 0 changed, 0 removed
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Doctest summary
===============
  387 tests
    0 failures in tests
    0 failures in setup code
    0 failures in cleanup code
build succeeded.

Testing of doctests in the sources finished, look at the results in build/doctest/output.txt.
   create-stamp debian/debhelper-build-stamp
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I: pbuilder-time-stamp: 1740196133