Artifact python-pybedtools_0.10.0-1+bd1_arm64-2024-10-07T01:38:39Z

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bd_uninstallable: null
filename: python-pybedtools_0.10.0-1+bd1_arm64-2024-10-07T01:38:39Z.build
source: python-pybedtools
version: 0.10.0-1

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python-pybedtools_0.10.0-1+bd1_arm64-2024-10-07T01:38:39Z.build
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sbuild (Debian sbuild) 0.85.11~bpo12+1 (31 August 2024) on debusine-worker-arm64-demeter-06.freexian.com

+==============================================================================+
| python-pybedtools 0.10.0-1+bd1 (arm64)       Mon, 07 Oct 2024 01:38:39 +0000 |
+==============================================================================+

Package: python-pybedtools
Version: 0.10.0-1+bd1
Source Version: 0.10.0-1
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: any

I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/834589/system.tar.xz to /tmp/tmp.sbuild.m2dZMlghtD...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Chroot Setup Commands                                                        |
+------------------------------------------------------------------------------+


rm -f /etc/resolv.conf
----------------------


I: Finished running 'rm -f /etc/resolv.conf'.

Finished processing commands.
--------------------------------------------------------------------------------
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+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

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Get:7 http://deb.debian.org/debian sid/main arm64 Components [4879 kB]
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0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

/tmp/debusine-fetch-exec-upload-hrwtdgq0/python-pybedtools_0.10.0-1.dsc exists in /tmp/debusine-fetch-exec-upload-hrwtdgq0; copying to chroot
I: NOTICE: Log filtering will replace 'build/python-pybedtools-f2boxq/python-pybedtools-0.10.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pybedtools-f2boxq' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), dh-sequence-python3, bedtools, cython3, python3-all-dev, python3-setuptools, python3-pysam, python3-matplotlib, python3-pytest, python3-numpy, python3-numpydoc, python3-pandas, python3-psutil, python3-yaml, python3-tk, python3-sphinx, r-base-core, zlib1g-dev, build-essential, fakeroot, dumb-init
Filtered Build-Depends: debhelper-compat (= 13), dh-sequence-python3, bedtools, cython3, python3-all-dev, python3-setuptools, python3-pysam, python3-matplotlib, python3-pytest, python3-numpy, python3-numpydoc, python3-pandas, python3-psutil, python3-yaml, python3-tk, python3-sphinx, r-base-core, zlib1g-dev, build-essential, fakeroot, dumb-init
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
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Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bedtools blt build-essential cpp
  cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dumb-init
  dwz fakeroot fontconfig fontconfig-config fonts-dejavu-core
  fonts-dejavu-mono fonts-lyx g++ g++-14 g++-14-aarch64-linux-gnu
  g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu
  gcc-aarch64-linux-gnu libasan8 libblas3 libc-dev-bin libc6-dev libcairo2
  libcc1-0 libcrypt-dev libcurl4t64 libdatrie1 libdebhelper-perl libdeflate0
  libelf1t64 libexpat1 libexpat1-dev libfakeroot
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
  libgcc-14-dev libgfortran5 libgraphite2-3 libharfbuzz0b libhts3t64
  libhtscodecs2 libhwasan0 libice6 libimagequant0 libisl23 libitm1 libjbig0
  libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc
  libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4
  liblsan0 libmpc3 libmpfr6 libncursesw6 libnsl2 libopenjp2-7 libpango-1.0-0
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
  libpng16-16t64 libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib
  libpython3.12t64 libpython3.13 libpython3.13-dev libpython3.13-minimal
  libpython3.13-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libsm6
  libstdc++-14-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common
  libtirpc3t64 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2
  libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxext6 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64
  linux-libc-dev m4 media-types po-debconf python-babel-localedata
  python-matplotlib-data python3 python3-alabaster python3-all python3-all-dev
  python3-appdirs python3-attr python3-autocommand python3-babel
  python3-brotli python3-certifi python3-chardet python3-charset-normalizer
  python3-contourpy python3-cycler python3-dateutil python3-decorator
  python3-defusedxml python3-dev python3-docutils python3-fonttools python3-fs
  python3-idna python3-imagesize python3-inflect python3-iniconfig
  python3-jaraco.context python3-jaraco.functools python3-jinja2
  python3-kiwisolver python3-lxml python3-lz4 python3-markupsafe
  python3-matplotlib python3-minimal python3-more-itertools python3-mpmath
  python3-numpy python3-numpydoc python3-packaging python3-pandas
  python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources
  python3-pluggy python3-psutil python3-pygments python3-pyparsing
  python3-pysam python3-pytest python3-requests python3-roman python3-scipy
  python3-setuptools python3-six python3-snowballstemmer python3-sphinx
  python3-sympy python3-tabulate python3-tk python3-typeguard
  python3-typing-extensions python3-tz python3-ufolib2 python3-urllib3
  python3-yaml python3-zipp python3.12 python3.12-dev python3.12-minimal
  python3.12-tk python3.13 python3.13-dev python3.13-minimal python3.13-tk
  r-base-core rpcsvc-proto sgml-base sphinx-common tk8.6-blt2.5 unicode-data
  x11-common xdg-utils xml-core zip zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales
  cpp-14-doc cython-doc dh-make flit python3-build python3-installer
  python3-wheel gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
  gdb-aarch64-linux-gnu libc-devtools glibc-doc libjs-jquery-ui-docs
  liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc libmail-box-perl python3-doc
  python3-venv python-attr-doc python-charset-normalizer-doc python-cycler-doc
  docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
  texlive-latex-base texlive-latex-recommended python-jinja2-doc
  python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript
  gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc
  python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5
  python3-sip python3-tornado texlive-extra-utils texlive-latex-extra
  python-mpmath-doc python3-gmpy2 gfortran python-numpy-doc python-pandas-doc
  python3-statsmodels python-pil-doc python-pygments-doc ttf-bitstream-vera
  python-pyparsing-doc python3-cryptography python3-openssl python3-socks
  python-requests-doc python-scipy-doc python-setuptools-doc python3-stemmer
  dvisvgm fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax
  python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-extra
  texlive-fonts-recommended texlive-plain-generic python-sympy-doc tix
  python3-tk-dbg python3.12-venv python3.12-doc binfmt-support python3.13-venv
  python3.13-doc elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html
  sgml-base-doc
Recommended packages:
  manpages manpages-dev libarchive-cpio-perl javascript-common libjson-xs-perl
  libgpm2 libltdl-dev libmail-sendmail-perl python3-bs4 python3-cssselect
  python3-html5lib python3-bottleneck python3-numexpr python3-odf
  python3-openpyxl python3-tables python3-olefile isympy-common r-recommended
  r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl
  libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bedtools blt build-essential cpp
  cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu cython3 debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism docutils-common dumb-init
  dwz fakeroot fontconfig fontconfig-config fonts-dejavu-core
  fonts-dejavu-mono fonts-lyx g++ g++-14 g++-14-aarch64-linux-gnu
  g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu
  gcc-aarch64-linux-gnu libasan8 libblas3 libc-dev-bin libc6-dev libcairo2
  libcc1-0 libcrypt-dev libcurl4t64 libdatrie1 libdebhelper-perl libdeflate0
  libelf1t64 libexpat1 libexpat1-dev libfakeroot
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
  libgcc-14-dev libgfortran5 libgraphite2-3 libharfbuzz0b libhts3t64
  libhtscodecs2 libhwasan0 libice6 libimagequant0 libisl23 libitm1 libjbig0
  libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc
  libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4
  liblsan0 libmpc3 libmpfr6 libncursesw6 libnsl2 libopenjp2-7 libpango-1.0-0
  libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0
  libpng16-16t64 libpython3-all-dev libpython3-dev libpython3-stdlib
  libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib
  libpython3.12t64 libpython3.13 libpython3.13-dev libpython3.13-minimal
  libpython3.13-stdlib libqhull-r8.0 libraqm0 libsharpyuv0 libsm6
  libstdc++-14-dev libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common
  libtirpc3t64 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2
  libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxext6 libxft2 libxrender1 libxslt1.1 libxss1 libxt6t64
  linux-libc-dev m4 media-types po-debconf python-babel-localedata
  python-matplotlib-data python3 python3-alabaster python3-all python3-all-dev
  python3-appdirs python3-attr python3-autocommand python3-babel
  python3-brotli python3-certifi python3-chardet python3-charset-normalizer
  python3-contourpy python3-cycler python3-dateutil python3-decorator
  python3-defusedxml python3-dev python3-docutils python3-fonttools python3-fs
  python3-idna python3-imagesize python3-inflect python3-iniconfig
  python3-jaraco.context python3-jaraco.functools python3-jinja2
  python3-kiwisolver python3-lxml python3-lz4 python3-markupsafe
  python3-matplotlib python3-minimal python3-more-itertools python3-mpmath
  python3-numpy python3-numpydoc python3-packaging python3-pandas
  python3-pandas-lib python3-pil python3-pil.imagetk python3-pkg-resources
  python3-pluggy python3-psutil python3-pygments python3-pyparsing
  python3-pysam python3-pytest python3-requests python3-roman python3-scipy
  python3-setuptools python3-six python3-snowballstemmer python3-sphinx
  python3-sympy python3-tabulate python3-tk python3-typeguard
  python3-typing-extensions python3-tz python3-ufolib2 python3-urllib3
  python3-yaml python3-zipp python3.12 python3.12-dev python3.12-minimal
  python3.12-tk python3.13 python3.13-dev python3.13-minimal python3.13-tk
  r-base-core rpcsvc-proto sbuild-build-depends-main-dummy sgml-base
  sphinx-common tk8.6-blt2.5 unicode-data x11-common xdg-utils xml-core zip
  zlib1g-dev
0 upgraded, 222 newly installed, 0 to remove and 0 not upgraded.
Need to get 179 MB/205 MB of archives.
After this operation, 853 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [1004 B]
Get:2 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-minimal 3.12.6-1+debusine1 [26.8 kB]
Get:3 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ libpython3-stdlib 3.12.6-1+debusine1 [9732 B]
Get:4 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3 3.12.6-1+debusine1 [27.8 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 libpython3.12-minimal arm64 3.12.7-1 [807 kB]
Get:6 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ cython3 3.0.11+dfsg-1+debusine1 [2724 kB]
Get:7 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ libpython3-dev 3.12.6-1+debusine1 [9992 B]
Get:8 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ libpython3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:9 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 python3.12-minimal arm64 3.12.7-1 [1941 kB]
Get:11 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python-matplotlib-data 3.8.3-3+bootstrap1 [2731 kB]
Get:12 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-all 3.12.6-1+debusine1 [1056 B]
Get:13 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-dev 3.12.6-1+debusine1 [26.1 kB]
Get:14 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-all-dev 3.12.6-1+debusine1 [1084 B]
Get:15 http://deb.debian.org/debian sid/main arm64 media-types all 10.1.0 [26.9 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2 [124 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3 [78.4 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 libnsl2 arm64 1.3.0-3+b2 [37.7 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 libpython3.12-stdlib arm64 3.12.7-1 [1901 kB]
Get:21 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-numpy 1:1.26.4+ds-11+bootstrap1 [3815 kB]
Get:22 http://deb.debian.org/debian sid/main arm64 python3.12 arm64 3.12.7-1 [671 kB]
Get:23 http://deb.debian.org/debian sid/main arm64 libpython3.13-minimal arm64 3.13.0~rc3-1 [849 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 python3.13-minimal arm64 3.13.0~rc3-1 [1835 kB]
Get:25 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-matplotlib 3.8.3-3+bootstrap1 [5583 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 sgml-base all 1.31 [15.4 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:32 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-pandas-lib 2.2.3+dfsg-1+bd1 [6020 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 bedtools arm64 2.31.1+dfsg-2 [588 kB]
Get:34 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-psutil 5.9.8-2+debusine1 [226 kB]
Get:35 http://deb.debian.org/debian sid/main arm64 libtcl8.6 arm64 8.6.15+dfsg-2 [982 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 libpng16-16t64 arm64 1.6.44-2 [273 kB]
Get:37 http://deb.debian.org/debian sid/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get:39 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-pysam 0.22.1+ds-2+debusine1 [3880 kB]
Get:40 file:/<<BUILDDIR>>/resolver-dc3Ilf/apt_archive ./ python3-yaml 6.0.2-1+debusine1 [149 kB]
Get:41 http://deb.debian.org/debian sid/main arm64 fonts-dejavu-core all 2.37-8 [840 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 fontconfig-config arm64 2.15.0-1.1 [317 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libfontconfig1 arm64 2.15.0-1.1 [385 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 libxau6 arm64 1:1.0.9-1+b1 [18.1 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3+b1 [24.3 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 libxcb1 arm64 1.17.0-2 [143 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 libx11-data all 2:1.8.7-1 [328 kB]
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Get:49 http://deb.debian.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1.1+b1 [27.0 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 libxft2 arm64 2.3.6-1+b1 [51.0 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 x11-common all 1:7.7+23.1 [216 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 libxss1 arm64 1:1.2.3-1+b1 [17.0 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 libtk8.6 arm64 8.6.15-1 [738 kB]
Get:55 http://deb.debian.org/debian sid/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [533 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 blt arm64 2.5.3+dfsg-7 [6024 B]
Get:57 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.10.12-1 [2400 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1 [59.7 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b1 [674 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b2 [50.2 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-6 [9165 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-6 [1280 B]
Get:67 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2 [4792 B]
Get:68 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.1.0-2 [1572 B]
Get:69 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-6 [42.3 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-6 [24.1 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-6 [2578 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-6 [1162 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-6 [2386 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-6 [1039 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-6 [1442 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-6 [2364 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-6 [17.7 MB]
Get:78 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-6 [515 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2 [1440 B]
Get:80 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.1.0-2 [5136 B]
Get:81 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-6 [2265 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-6 [10.1 MB]
Get:83 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-6 [19.9 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2 [1200 B]
Get:85 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.1.0-2 [1328 B]
Get:86 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.10 [4516 B]
Get:87 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-7 [517 kB]
Get:89 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:91 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:92 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.191-2 [188 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 python3-more-itertools all 10.5.0-1 [63.8 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 python3-typing-extensions all 4.12.2-2 [73.0 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 python3-typeguard all 4.3.0-1 [36.5 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 python3-inflect all 7.3.1-2 [32.4 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 python3-jaraco.context all 6.0.0-1 [7984 B]
Get:102 http://deb.debian.org/debian sid/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 python3-pkg-resources all 74.1.2-2 [213 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 python3-zipp all 3.20.2-1 [10.3 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 python3-setuptools all 74.1.2-2 [736 kB]
Get:106 http://deb.debian.org/debian sid/main arm64 dh-python all 6.20240824 [109 kB]
Get:107 http://deb.debian.org/debian sid/main arm64 xml-core all 0.19 [20.1 kB]
Get:108 http://deb.debian.org/debian sid/main arm64 docutils-common all 0.21.2+dfsg-2 [128 kB]
Get:109 http://deb.debian.org/debian sid/main arm64 dumb-init arm64 1.2.5-3 [13.4 kB]
Get:110 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:111 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:112 http://deb.debian.org/debian sid/main arm64 fontconfig arm64 2.15.0-1.1 [462 kB]
Get:113 http://deb.debian.org/debian sid/main arm64 fonts-lyx all 2.4.2.1-1 [190 kB]
Get:114 http://deb.debian.org/debian sid/main arm64 libblas3 arm64 3.12.0-3 [91.7 kB]
Get:115 http://deb.debian.org/debian sid/main arm64 libpixman-1-0 arm64 0.42.2-1+b1 [477 kB]
Get:116 http://deb.debian.org/debian sid/main arm64 libxcb-render0 arm64 1.17.0-2 [115 kB]
Get:117 http://deb.debian.org/debian sid/main arm64 libxcb-shm0 arm64 1.17.0-2 [105 kB]
Get:118 http://deb.debian.org/debian sid/main arm64 libcairo2 arm64 1.18.2-2 [483 kB]
Get:119 http://deb.debian.org/debian sid/main arm64 libcurl4t64 arm64 8.10.1-1 [322 kB]
Get:120 http://deb.debian.org/debian sid/main arm64 libdatrie1 arm64 0.2.13-3 [37.2 kB]
Get:121 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.21-1 [42.2 kB]
Get:122 http://deb.debian.org/debian sid/main arm64 libexpat1-dev arm64 2.6.3-1 [142 kB]
Get:123 http://deb.debian.org/debian sid/main arm64 libfribidi0 arm64 1.0.15-1 [71.8 kB]
Get:124 http://deb.debian.org/debian sid/main arm64 libgfortran5 arm64 14.2.0-6 [361 kB]
Get:125 http://deb.debian.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-2 [69.2 kB]
Get:126 http://deb.debian.org/debian sid/main arm64 libharfbuzz0b arm64 9.0.0-1 [441 kB]
Get:127 http://deb.debian.org/debian sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get:128 http://deb.debian.org/debian sid/main arm64 libhts3t64 arm64 1.20+ds-1 [416 kB]
Get:129 http://deb.debian.org/debian sid/main arm64 libice6 arm64 2:1.0.10-1+b1 [53.7 kB]
Get:130 http://deb.debian.org/debian sid/main arm64 libimagequant0 arm64 2.18.0-1+b1 [34.6 kB]
Get:131 http://deb.debian.org/debian sid/main arm64 libjbig0 arm64 2.1-6.1+b1 [30.4 kB]
Get:132 http://deb.debian.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.1.5-3 [172 kB]
Get:133 http://deb.debian.org/debian sid/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:134 http://deb.debian.org/debian sid/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:135 http://deb.debian.org/debian sid/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:136 http://deb.debian.org/debian sid/main arm64 libjs-sphinxdoc all 7.4.7-3 [158 kB]
Get:137 http://deb.debian.org/debian sid/main arm64 libjson-perl all 4.10000-1 [87.5 kB]
Get:138 http://deb.debian.org/debian sid/main arm64 liblapack3 arm64 3.12.0-3 [1757 kB]
Get:139 http://deb.debian.org/debian sid/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1+b1 [25.0 kB]
Get:140 http://deb.debian.org/debian sid/main arm64 liblcms2-2 arm64 2.14-2+b1 [144 kB]
Get:141 http://deb.debian.org/debian sid/main arm64 liblerc4 arm64 4.0.0+ds-4+b1 [142 kB]
Get:142 http://deb.debian.org/debian sid/main arm64 libopenjp2-7 arm64 2.5.0-2+b3 [177 kB]
Get:143 http://deb.debian.org/debian sid/main arm64 libthai-data all 0.1.29-2 [168 kB]
Get:144 http://deb.debian.org/debian sid/main arm64 libthai0 arm64 0.1.29-2 [48.0 kB]
Get:145 http://deb.debian.org/debian sid/main arm64 libpango-1.0-0 arm64 1.54.0+ds-2 [210 kB]
Get:146 http://deb.debian.org/debian sid/main arm64 libpangoft2-1.0-0 arm64 1.54.0+ds-2 [51.8 kB]
Get:147 http://deb.debian.org/debian sid/main arm64 libpangocairo-1.0-0 arm64 1.54.0+ds-2 [33.4 kB]
Get:148 http://deb.debian.org/debian sid/main arm64 libpaper1 arm64 1.1.29+b1 [12.9 kB]
Get:149 http://deb.debian.org/debian sid/main arm64 libpaper-utils arm64 1.1.29+b1 [9068 B]
Get:150 http://deb.debian.org/debian sid/main arm64 libpython3.12t64 arm64 3.12.7-1 [1982 kB]
Get:151 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB]
Get:152 http://deb.debian.org/debian sid/main arm64 libpython3.12-dev arm64 3.12.7-1 [4793 kB]
Get:153 http://deb.debian.org/debian sid/main arm64 libpython3.13-stdlib arm64 3.13.0~rc3-1 [1920 kB]
Get:154 http://deb.debian.org/debian sid/main arm64 libpython3.13 arm64 3.13.0~rc3-1 [1959 kB]
Get:155 http://deb.debian.org/debian sid/main arm64 libpython3.13-dev arm64 3.13.0~rc3-1 [4668 kB]
Get:156 http://deb.debian.org/debian sid/main arm64 libqhull-r8.0 arm64 2020.2-6+b1 [226 kB]
Get:157 http://deb.debian.org/debian sid/main arm64 libraqm0 arm64 0.10.1-1+b1 [13.7 kB]
Get:158 http://deb.debian.org/debian sid/main arm64 libsharpyuv0 arm64 1.4.0-0.1 [111 kB]
Get:159 http://deb.debian.org/debian sid/main arm64 libsm6 arm64 2:1.2.3-1+b1 [32.7 kB]
Get:160 http://deb.debian.org/debian sid/main arm64 libwebp7 arm64 1.4.0-0.1 [267 kB]
Get:161 http://deb.debian.org/debian sid/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB]
Get:162 http://deb.debian.org/debian sid/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [110 kB]
Get:163 http://deb.debian.org/debian sid/main arm64 libwebpmux3 arm64 1.4.0-0.1 [122 kB]
Get:164 http://deb.debian.org/debian sid/main arm64 libxslt1.1 arm64 1.1.35-1.1 [221 kB]
Get:165 http://deb.debian.org/debian sid/main arm64 libxt6t64 arm64 1:1.2.1-1.2 [172 kB]
Get:166 http://deb.debian.org/debian sid/main arm64 python-babel-localedata all 2.14.0-1 [5701 kB]
Get:167 http://deb.debian.org/debian sid/main arm64 python3-alabaster all 0.7.16-0.1 [27.9 kB]
Get:168 http://deb.debian.org/debian sid/main arm64 python3.13 arm64 3.13.0~rc3-1 [730 kB]
Get:169 http://deb.debian.org/debian sid/main arm64 python3.12-dev arm64 3.12.7-1 [505 kB]
Get:170 http://deb.debian.org/debian sid/main arm64 python3.13-dev arm64 3.13.0~rc3-1 [504 kB]
Get:171 http://deb.debian.org/debian sid/main arm64 python3-appdirs all 1.4.4-4 [12.5 kB]
Get:172 http://deb.debian.org/debian sid/main arm64 python3-attr all 24.2.0-1 [68.4 kB]
Get:173 http://deb.debian.org/debian sid/main arm64 python3-tz all 2024.1-2 [30.9 kB]
Get:174 http://deb.debian.org/debian sid/main arm64 python3-babel all 2.14.0-1 [111 kB]
Get:175 http://deb.debian.org/debian sid/main arm64 python3-brotli arm64 1.1.0-2+b4 [301 kB]
Get:176 http://deb.debian.org/debian sid/main arm64 python3-certifi all 2024.8.30-1 [159 kB]
Get:177 http://deb.debian.org/debian sid/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:178 http://deb.debian.org/debian sid/main arm64 python3-charset-normalizer arm64 3.3.2-4 [110 kB]
Get:179 http://deb.debian.org/debian sid/main arm64 python3-contourpy arm64 1.3.0-2 [191 kB]
Get:180 http://deb.debian.org/debian sid/main arm64 python3-cycler all 0.12.1-1 [9496 B]
Get:181 http://deb.debian.org/debian sid/main arm64 python3-dateutil all 2.9.0-3 [79.3 kB]
Get:182 http://deb.debian.org/debian sid/main arm64 python3-decorator all 5.1.1-5 [15.1 kB]
Get:183 http://deb.debian.org/debian sid/main arm64 python3-defusedxml all 0.7.1-2 [43.3 kB]
Get:184 http://deb.debian.org/debian sid/main arm64 python3-roman all 4.2-1 [10.4 kB]
Get:185 http://deb.debian.org/debian sid/main arm64 python3-docutils all 0.21.2+dfsg-2 [403 kB]
Get:186 http://deb.debian.org/debian sid/main arm64 python3-scipy arm64 1.13.1-5 [15.4 MB]
Get:187 http://deb.debian.org/debian sid/main arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB]
Get:188 http://deb.debian.org/debian sid/main arm64 python3-mpmath all 1.3.0-1 [419 kB]
Get:189 http://deb.debian.org/debian sid/main arm64 python3-sympy all 1.13.3-1 [4147 kB]
Get:190 http://deb.debian.org/debian sid/main arm64 python3-six all 1.16.0-7 [16.4 kB]
Get:191 http://deb.debian.org/debian sid/main arm64 python3-fs all 2.4.16-4 [95.4 kB]
Get:192 http://deb.debian.org/debian sid/main arm64 python3-lxml arm64 5.3.0-1 [1096 kB]
Get:193 http://deb.debian.org/debian sid/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b4 [25.1 kB]
Get:194 http://deb.debian.org/debian sid/main arm64 unicode-data all 15.1.0-1 [8547 kB]
Get:195 http://deb.debian.org/debian sid/main arm64 python3-fonttools arm64 4.46.0-1+b1 [1319 kB]
Get:196 http://deb.debian.org/debian sid/main arm64 python3-idna all 3.8-2 [41.6 kB]
Get:197 http://deb.debian.org/debian sid/main arm64 python3-imagesize all 1.4.1-1 [6688 B]
Get:198 http://deb.debian.org/debian sid/main arm64 python3-iniconfig all 1.1.1-2 [6396 B]
Get:199 http://deb.debian.org/debian sid/main arm64 python3-markupsafe arm64 2.1.5-1+b1 [13.7 kB]
Get:200 http://deb.debian.org/debian sid/main arm64 python3-jinja2 all 3.1.3-1 [119 kB]
Get:201 http://deb.debian.org/debian sid/main arm64 python3-kiwisolver arm64 1.4.7-1 [55.4 kB]
Get:202 http://deb.debian.org/debian sid/main arm64 python3-pil arm64 10.4.0-1 [480 kB]
Get:203 http://deb.debian.org/debian sid/main arm64 python3.12-tk arm64 3.12.7-1 [110 kB]
Get:204 http://deb.debian.org/debian sid/main arm64 python3.13-tk arm64 3.13.0~rc3-1 [101 kB]
Get:205 http://deb.debian.org/debian sid/main arm64 python3-tk arm64 3.12.6-1 [9428 B]
Get:206 http://deb.debian.org/debian sid/main arm64 python3-pil.imagetk arm64 10.4.0-1 [79.4 kB]
Get:207 http://deb.debian.org/debian sid/main arm64 python3-pyparsing all 3.1.2-1 [146 kB]
Get:208 http://deb.debian.org/debian sid/main arm64 python3-packaging all 24.1-1 [45.8 kB]
Get:209 http://deb.debian.org/debian sid/main arm64 sphinx-common all 7.4.7-3 [731 kB]
Get:210 http://deb.debian.org/debian sid/main arm64 python3-pygments all 2.18.0+dfsg-1 [836 kB]
Get:211 http://deb.debian.org/debian sid/main arm64 python3-urllib3 all 2.0.7-2 [111 kB]
Get:212 http://deb.debian.org/debian sid/main arm64 python3-requests all 2.32.3+dfsg-1 [71.9 kB]
Get:213 http://deb.debian.org/debian sid/main arm64 python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get:214 http://deb.debian.org/debian sid/main arm64 python3-sphinx all 7.4.7-3 [588 kB]
Get:215 http://deb.debian.org/debian sid/main arm64 python3-tabulate all 0.9.0-1 [45.9 kB]
Get:216 http://deb.debian.org/debian sid/main arm64 python3-numpydoc all 1.6.0-2 [49.6 kB]
Get:217 http://deb.debian.org/debian sid/main arm64 python3-pandas all 2.2.3+dfsg-1 [3096 kB]
Get:218 http://deb.debian.org/debian sid/main arm64 python3-pluggy all 1.5.0-1 [26.9 kB]
Get:219 http://deb.debian.org/debian sid/main arm64 python3-pytest all 8.3.3-1 [249 kB]
Get:220 http://deb.debian.org/debian sid/main arm64 zip arm64 3.0-14 [225 kB]
Get:221 http://deb.debian.org/debian sid/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:222 http://deb.debian.org/debian sid/main arm64 r-base-core arm64 4.4.1-3 [28.0 MB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 179 MB in 2s (102 MB/s)
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Unpacking libpython3.12-minimal:arm64 (3.12.7-1) ...
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Setting up libpython3.12-minimal:arm64 (3.12.7-1) ...
Setting up libexpat1:arm64 (2.6.3-1) ...
Setting up python3.12-minimal (3.12.7-1) ...
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Unpacking python3-minimal (3.12.6-1+debusine1) ...
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Unpacking libncursesw6:arm64 (6.5-2) ...
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Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3) ...
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Unpacking libpython3.12-stdlib:arm64 (3.12.7-1) ...
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Unpacking python3.12 (3.12.7-1) ...
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Unpacking libpython3-stdlib:arm64 (3.12.6-1+debusine1) ...
Setting up python3-minimal (3.12.6-1+debusine1) ...
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Unpacking python3 (3.12.6-1+debusine1) ...
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Unpacking libpython3.13-minimal:arm64 (3.13.0~rc3-1) ...
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Unpacking python3.13-minimal (3.13.0~rc3-1) ...
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Unpacking autopoint (0.22.5-2) ...
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Setting up libharfbuzz0b:arm64 (9.0.0-1) ...
Setting up libxss1:arm64 (1:1.2.3-1+b1) ...
Setting up libfontconfig1:arm64 (2.15.0-1.1) ...
Setting up libgcc-14-dev:arm64 (14.2.0-6) ...
Setting up libstdc++-14-dev:arm64 (14.2.0-6) ...
Setting up libsm6:arm64 (2:1.2.3-1+b1) ...
Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1+b1) ...
Setting up fontconfig (2.15.0-1.1) ...
Regenerating fonts cache... done.
Setting up libxft2:arm64 (2.3.6-1+b1) ...
Setting up libpython3.12-stdlib:arm64 (3.12.7-1) ...
Setting up libtk8.6:arm64 (8.6.15-1) ...
Setting up python3.12 (3.12.7-1) ...
Setting up libpango-1.0-0:arm64 (1.54.0+ds-2) ...
Setting up python3.12-tk (3.12.7-1) ...
Setting up libcairo2:arm64 (1.18.2-2) ...
Setting up python3.13-tk (3.13.0~rc3-1) ...
Setting up libpython3.12t64:arm64 (3.12.7-1) ...
Setting up cpp-aarch64-linux-gnu (4:14.1.0-2) ...
Setting up libexpat1-dev:arm64 (2.6.3-1) ...
Setting up libraqm0:arm64 (0.10.1-1+b1) ...
Setting up sphinx-common (7.4.7-3) ...
Setting up libxt6t64:arm64 (1:1.2.1-1.2) ...
Setting up cpp-14 (14.2.0-6) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ...
Setting up cpp (4:14.1.0-2) ...
Setting up gcc-14-aarch64-linux-gnu (14.2.0-6) ...
Setting up libpangoft2-1.0-0:arm64 (1.54.0+ds-2) ...
Setting up libpangocairo-1.0-0:arm64 (1.54.0+ds-2) ...
Setting up libpython3-stdlib:arm64 (3.12.6-1+debusine1) ...
Setting up gcc-aarch64-linux-gnu (4:14.1.0-2) ...
Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ...
Setting up g++-14-aarch64-linux-gnu (14.2.0-6) ...
Setting up blt (2.5.3+dfsg-7) ...
Setting up python3 (3.12.6-1+debusine1) ...
Setting up libpython3.12-dev:arm64 (3.12.7-1) ...
Setting up python3-zipp (3.20.2-1) ...
Setting up python3-autocommand (2.2.2-3) ...
Setting up python3-markupsafe (2.1.5-1+b1) ...
Setting up python3-psutil (5.9.8-2+debusine1) ...
Setting up python3-tz (2024.1-2) ...
Setting up gcc-14 (14.2.0-6) ...
Setting up python3-six (1.16.0-7) ...
Setting up python3-pil:arm64 (10.4.0-1) ...
Setting up python3-roman (4.2-1) ...
Setting up python3-decorator (5.1.1-5) ...
Setting up python3-jinja2 (3.1.3-1) ...
Setting up python3-packaging (24.1-1) ...
Setting up python3-pyparsing (3.1.2-1) ...
Setting up python3-certifi (2024.8.30-1) ...
Setting up python3-snowballstemmer (2.2.0-4) ...
Setting up python3-brotli (1.1.0-2+b4) ...
Setting up libpython3.13-dev:arm64 (3.13.0~rc3-1) ...
Setting up python3-cycler (0.12.1-1) ...
Setting up r-base-core (4.4.1-3) ...

Creating config file /etc/R/Renviron with new version
Setting up python3-kiwisolver (1.4.7-1) ...
Setting up python3-idna (3.8-2) ...
Setting up python3.12-dev (3.12.7-1) ...
Setting up cython3 (3.0.11+dfsg-1+debusine1) ...
Setting up python3-typing-extensions (4.12.2-2) ...
Setting up python3-urllib3 (2.0.7-2) ...
Setting up python3-pluggy (1.5.0-1) ...
Setting up python3-lxml:arm64 (5.3.0-1) ...
Setting up g++-aarch64-linux-gnu (4:14.1.0-2) ...
Setting up python3-dateutil (2.9.0-3) ...
Setting up g++-14 (14.2.0-6) ...
Setting up python3-mpmath (1.3.0-1) ...
Setting up python3-appdirs (1.4.4-4) ...
Setting up python3-imagesize (1.4.1-1) ...
Setting up python3-more-itertools (10.5.0-1) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-sympy (1.13.3-1) ...
Setting up python3-attr (24.2.0-1) ...
Setting up python3-pysam (0.22.1+ds-2+debusine1) ...
Setting up libpython3-dev:arm64 (3.12.6-1+debusine1) ...
Setting up python3-jaraco.functools (4.1.0-1) ...
Setting up python3-jaraco.context (6.0.0-1) ...
Setting up libtool (2.4.7-7) ...
Setting up python3-lz4 (4.0.2+dfsg-1+b4) ...
Setting up python3-defusedxml (0.7.1-2) ...
Setting up python3-charset-normalizer (3.3.2-4) ...
Setting up python3.13-dev (3.13.0~rc3-1) ...
Setting up python3-pytest (8.3.3-1) ...
Setting up python3-alabaster (0.7.16-0.1) ...
Setting up python3-typeguard (4.3.0-1) ...
Setting up python3-tabulate (0.9.0-1) ...
Setting up python3-all (3.12.6-1+debusine1) ...
Setting up python3-yaml (6.0.2-1+debusine1) ...
Setting up python3-tk:arm64 (3.12.6-1) ...
Setting up gcc (4:14.1.0-2) ...
Setting up dh-autoreconf (20) ...
Setting up python3-inflect (7.3.1-2) ...
Setting up python3-pil.imagetk:arm64 (10.4.0-1) ...
Setting up libpython3-all-dev:arm64 (3.12.6-1+debusine1) ...
Setting up python3-dev (3.12.6-1+debusine1) ...
Setting up g++ (4:14.1.0-2) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up build-essential (12.10) ...
Setting up python3-pkg-resources (74.1.2-2) ...
Setting up python3-all-dev (3.12.6-1+debusine1) ...
Setting up python3-setuptools (74.1.2-2) ...
Setting up python3-babel (2.14.0-1) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up debhelper (13.20) ...
Setting up python3-fs (2.4.16-4) ...
Setting up python3-pygments (2.18.0+dfsg-1) ...
Setting up python3-chardet (5.2.0+dfsg-1) ...
Setting up python3-requests (2.32.3+dfsg-1) ...
Setting up python3-numpy (1:1.26.4+ds-11+bootstrap1) ...
Setting up python3-contourpy (1.3.0-2) ...
Setting up dh-python (6.20240824) ...
Setting up python3-scipy (1.13.1-5) ...
Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-1+bd1) ...
Setting up python3-pandas (2.2.3+dfsg-1) ...
Setting up python3-fonttools (4.46.0-1+b1) ...
Setting up python3-ufolib2 (0.16.0+dfsg1-1) ...
Setting up python3-matplotlib (3.8.3-3+bootstrap1) ...
Processing triggers for libc-bin (2.40-3) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for sgml-base (1.31) ...
Setting up docutils-common (0.21.2+dfsg-2) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.21.2+dfsg-2) ...
Setting up python3-sphinx (7.4.7-3) ...
Setting up python3-numpydoc (1.6.0-2) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (arm64 included in any all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-6 gcc-14_14.2.0-6 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-6 libstdc++6_14.2.0-6 linux-libc-dev_6.10.12-1
Package versions: appstream_1.0.3-1 apt_2.9.8 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.5 base-passwd_3.6.4 bash_5.2.32-1+b1 bedtools_2.31.1+dfsg-2 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 blt_2.5.3+dfsg-7 bsdextrautils_2.40.2-9 bsdutils_1:2.40.2-9 build-essential_12.10 bzip2_1.0.8-6 ca-certificates_20240203 coreutils_9.4-3.1 cpp_4:14.1.0-2 cpp-14_14.2.0-6 cpp-14-aarch64-linux-gnu_14.2.0-6 cpp-aarch64-linux-gnu_4:14.1.0-2 cython3_3.0.11+dfsg-1+debusine1 dash_0.5.12-9 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.20 dh-autoreconf_20 dh-python_6.20240824 dh-strip-nondeterminism_1.14.0-1 diffstat_1.66-1 diffutils_1:3.10-1 docutils-common_0.21.2+dfsg-2 dpkg_1.22.11 dpkg-dev_1.22.11 dumb-init_1.2.5-3 dwz_0.15-1+b1 e2fsprogs_1.47.1-1 fakeroot_1.36-1 file_1:5.45-3 findutils_4.10.0-3 fontconfig_2.15.0-1.1 fontconfig-config_2.15.0-1.1 fonts-dejavu-core_2.37-8 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libtcl8.6_8.6.15+dfsg-2 libterm-readkey-perl_2.38-2+b3 libtext-glob-perl_0.11-3 libtext-levenshteinxs-perl_0.03-5+b3 libtext-markdown-discount-perl_0.16-1+b2 libtext-xslate-perl_3.5.9-2 libthai-data_0.1.29-2 libthai0_0.1.29-2 libtiff6_4.5.1+git230720-5 libtime-duration-perl_1.21-2 libtime-moment-perl_0.44-2+b3 libtimedate-perl_2.3300-2 libtinfo6_6.5-2 libtirpc-common_1.3.4+ds-1.3 libtirpc3t64_1.3.4+ds-1.3 libtk8.6_8.6.15-1 libtool_2.4.7-7 libtry-tiny-perl_0.32-1 libtsan2_14.2.0-6 libubsan1_14.2.0-6 libuchardet0_0.0.8-1+b1 libudev1_256.6-1 libunicode-utf8-perl_0.62-2+b2 libunistring5_1.2-1 liburi-perl_5.29-1 libuuid1_2.40.2-9 libvariable-magic-perl_0.64-1 libwebp7_1.4.0-0.1 libwebpdemux2_1.4.0-0.1 libwebpmux3_1.4.0-0.1 libwww-mechanize-perl_2.19-1 libwww-perl_6.77-1 libwww-robotrules-perl_6.02-1 libx11-6_2:1.8.7-1+b1 libx11-data_2:1.8.7-1 libxau6_1:1.0.9-1+b1 libxcb-render0_1.17.0-2 libxcb-shm0_1.17.0-2 libxcb1_1.17.0-2 libxdmcp6_1:1.1.2-3+b1 libxext6_2:1.3.4-1+b1 libxft2_2.3.6-1+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-5 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml2_2.12.7+dfsg+really2.9.14-0.1 libxmlb2_0.3.19-1 libxrender1_1:0.9.10-1.1+b1 libxs-parse-keyword-perl_0.46-1 libxslt1.1_1.1.35-1.1 libxss1_1:1.2.3-1+b1 libxt6t64_1:1.2.1-1.2 libxxhash0_0.8.2-2+b1 libyaml-0-2_0.2.5-1+b1 libyaml-libyaml-perl_0.902.0+ds-2 libzstd1_1.5.6+dfsg-1 lintian_2.119.0 linux-libc-dev_6.10.12-1 login_1:4.16.0-2+really2.40.2-9 login.defs_1:4.16.0-4 logsave_1.47.1-1 lzop_1.04-2 m4_1.4.19-4 make_4.3-4.1 man-db_2.13.0-1 mawk_1.3.4.20240905-1 media-types_10.1.0 mount_2.40.2-9 ncurses-base_6.5-2 ncurses-bin_6.5-2 netbase_6.4 openssl_3.3.2-1 openssl-provider-legacy_3.3.2-1 passwd_1:4.16.0-4 patch_2.7.6-7 patchutils_0.4.2-1 perl_5.38.2-5 perl-base_5.38.2-5 perl-modules-5.38_5.38.2-5 perl-openssl-defaults_7+b2 plzip_1.11-2 po-debconf_1.0.21+nmu1 python-babel-localedata_2.14.0-1 python-matplotlib-data_3.8.3-3+bootstrap1 python3_3.12.6-1+debusine1 python3-alabaster_0.7.16-0.1 python3-all_3.12.6-1+debusine1 python3-all-dev_3.12.6-1+debusine1 python3-appdirs_1.4.4-4 python3-attr_24.2.0-1 python3-autocommand_2.2.2-3 python3-babel_2.14.0-1 python3-brotli_1.1.0-2+b4 python3-certifi_2024.8.30-1 python3-chardet_5.2.0+dfsg-1 python3-charset-normalizer_3.3.2-4 python3-contourpy_1.3.0-2 python3-cycler_0.12.1-1 python3-dateutil_2.9.0-3 python3-decorator_5.1.1-5 python3-defusedxml_0.7.1-2 python3-dev_3.12.6-1+debusine1 python3-docutils_0.21.2+dfsg-2 python3-fonttools_4.46.0-1+b1 python3-fs_2.4.16-4 python3-idna_3.8-2 python3-imagesize_1.4.1-1 python3-inflect_7.3.1-2 python3-iniconfig_1.1.1-2 python3-jaraco.context_6.0.0-1 python3-jaraco.functools_4.1.0-1 python3-jinja2_3.1.3-1 python3-kiwisolver_1.4.7-1 python3-lxml_5.3.0-1 python3-lz4_4.0.2+dfsg-1+b4 python3-markupsafe_2.1.5-1+b1 python3-matplotlib_3.8.3-3+bootstrap1 python3-minimal_3.12.6-1+debusine1 python3-more-itertools_10.5.0-1 python3-mpmath_1.3.0-1 python3-numpy_1:1.26.4+ds-11+bootstrap1 python3-numpydoc_1.6.0-2 python3-packaging_24.1-1 python3-pandas_2.2.3+dfsg-1 python3-pandas-lib_2.2.3+dfsg-1+bd1 python3-pil_10.4.0-1 python3-pil.imagetk_10.4.0-1 python3-pkg-resources_74.1.2-2 python3-pluggy_1.5.0-1 python3-psutil_5.9.8-2+debusine1 python3-pygments_2.18.0+dfsg-1 python3-pyparsing_3.1.2-1 python3-pysam_0.22.1+ds-2+debusine1 python3-pytest_8.3.3-1 python3-requests_2.32.3+dfsg-1 python3-roman_4.2-1 python3-scipy_1.13.1-5 python3-setuptools_74.1.2-2 python3-six_1.16.0-7 python3-snowballstemmer_2.2.0-4 python3-sphinx_7.4.7-3 python3-sympy_1.13.3-1 python3-tabulate_0.9.0-1 python3-tk_3.12.6-1 python3-typeguard_4.3.0-1 python3-typing-extensions_4.12.2-2 python3-tz_2024.1-2 python3-ufolib2_0.16.0+dfsg1-1 python3-urllib3_2.0.7-2 python3-yaml_6.0.2-1+debusine1 python3-zipp_3.20.2-1 python3.12_3.12.7-1 python3.12-dev_3.12.7-1 python3.12-minimal_3.12.7-1 python3.12-tk_3.12.7-1 python3.13_3.13.0~rc3-1 python3.13-dev_3.13.0~rc3-1 python3.13-minimal_3.13.0~rc3-1 python3.13-tk_3.13.0~rc3-1 r-base-core_4.4.1-3 readline-common_8.2-5 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sgml-base_1.31 shared-mime-info_2.4-5+b1 sphinx-common_7.4.7-3 sysvinit-utils_3.10-2 t1utils_1.41-4 tar_1.35+dfsg-3 tk8.6-blt2.5_2.5.3+dfsg-7 tzdata_2024b-2 ucf_3.0043+nmu1 unicode-data_15.1.0-1 unzip_6.0-28 util-linux_2.40.2-9 x11-common_1:7.7+23.1 xdg-utils_1.1.3-4.1 xml-core_0.19 xz-utils_5.6.2-2 zip_3.0-14 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

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Hash: SHA512

Format: 3.0 (quilt)
Source: python-pybedtools
Binary: pybedtools-bin, python3-pybedtools, python-pybedtools-doc
Architecture: any all
Version: 0.10.0-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe@debian.org>, Steffen Moeller <moeller@debian.org>
Homepage: https://daler.github.io/pybedtools/
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-pybedtools
Vcs-Git: https://salsa.debian.org/med-team/python-pybedtools.git
Testsuite: autopkgtest-pkg-python
Build-Depends: debhelper-compat (= 13), dh-sequence-python3, bedtools, cython3, python3-all-dev, python3-setuptools, python3-pysam, python3-matplotlib, python3-pytest, python3-numpy, python3-numpydoc, python3-pandas, python3-psutil, python3-yaml, python3-tk, python3-sphinx, r-base-core, zlib1g-dev
Package-List:
 pybedtools-bin deb python optional arch=all
 python-pybedtools-doc deb doc optional arch=all
 python3-pybedtools deb python optional arch=any
Checksums-Sha1:
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 1925bafb451d10fa2d2473c13a7700574f84fc3e 30020 python-pybedtools_0.10.0-1.debian.tar.xz
Checksums-Sha256:
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Files:
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 64503c63fc9ed541eaa5d67a304685cb 30020 python-pybedtools_0.10.0-1.debian.tar.xz

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gpgv: Signature made Fri May  3 16:31:52 2024 UTC
gpgv:                using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.10.0-1.dsc: no acceptable signature found
dpkg-source: info: extracting python-pybedtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking python-pybedtools_0.10.0.orig.tar.xz
dpkg-source: info: unpacking python-pybedtools_0.10.0-1.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

Check disk space
----------------

Sufficient free space for build

Hack binNMU version
-------------------

Created changelog entry for binNMU version 0.10.0-1+bd1

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SHELL=/bin/sh
USER=debusine-worker

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -mDebusine Rebuild <debusine@example.net> -B -rfakeroot
dpkg-buildpackage: info: source package python-pybedtools
dpkg-buildpackage: info: source version 0.10.0-1+bd1
dpkg-buildpackage: info: source distribution sid
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
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 '/<<PKGBUILDDIR>>'
/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 '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary-arch
dh binary-arch --with python3,sphinxdoc --buildsystem=pybuild
   dh_update_autotools_config -a -O--buildsystem=pybuild
   dh_autoreconf -a -O--buildsystem=pybuild
   dh_auto_configure -a -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py config 
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running config
I: pybuild base:311: python3.12 setup.py config 
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
python3 setup.py cythonize
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running cythonize
/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: /<<PKGBUILDDIR>>/pybedtools/cbedtools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
Compiling pybedtools/cbedtools.pyx because it changed.
Compiling pybedtools/featurefuncs.pyx because it changed.
[1/2] Cythonizing pybedtools/cbedtools.pyx
[2/2] Cythonizing pybedtools/featurefuncs.pyx
dh_auto_build
I: pybuild base:311: /usr/bin/python3.13 setup.py build 
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/helpers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/genome_registry.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/filenames.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/logger.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/parallel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/settings.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/paths.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/bedtool.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_contrib.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_pathlib.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_iter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/regression_tests.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_1.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_helpers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_len_leak.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_issues.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/tfuncs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
running egg_info
creating pybedtools.egg-info
writing pybedtools.egg-info/PKG-INFO
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pybedtools'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _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 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/cbedtools.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/cbedtools.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/cbedtools.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/featurefuncs.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
copying pybedtools/featurefuncs.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include
copying pybedtools/include/bedFile.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include
copying pybedtools/include/bedFile.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include
copying pybedtools/include/fileType.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include
copying pybedtools/include/fileType.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include
copying pybedtools/include/gzstream.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include
copying pybedtools/include/gzstream.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include
copying pybedtools/test/data/small.fastq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/b.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/x.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/d.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/x.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/small.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/c.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/y.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/mpl-expected.png -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_cases.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
creating build
creating build/temp.linux-aarch64-cpython-313
creating build/temp.linux-aarch64-cpython-313/pybedtools
creating build/temp.linux-aarch64-cpython-313/pybedtools/include
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/cbedtools.cpp -o build/temp.linux-aarch64-cpython-313/pybedtools/cbedtools.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-313/pybedtools/include/bedFile.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-313/pybedtools/include/fileType.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-313/pybedtools/include/gzstream.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/pybedtools/cbedtools.o build/temp.linux-aarch64-cpython-313/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-313/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/aarch64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/cbedtools.cpython-313-aarch64-linux-gnu.so
building 'pybedtools.featurefuncs' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/featurefuncs.cpp -o build/temp.linux-aarch64-cpython-313/pybedtools/featurefuncs.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-313/pybedtools/include/bedFile.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-313/pybedtools/include/fileType.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-313/pybedtools/include/gzstream.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-313/pybedtools/featurefuncs.o build/temp.linux-aarch64-cpython-313/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-313/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/aarch64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/featurefuncs.cpython-313-aarch64-linux-gnu.so
I: pybuild base:311: /usr/bin/python3 setup.py build 
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/helpers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/genome_registry.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/filenames.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/logger.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/parallel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/settings.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/paths.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/bedtool.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_contrib.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_pathlib.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_iter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/regression_tests.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_1.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_helpers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_len_leak.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_issues.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/tfuncs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/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:218: _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 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/cbedtools.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/cbedtools.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/cbedtools.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/featurefuncs.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
copying pybedtools/featurefuncs.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include
copying pybedtools/include/bedFile.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include
copying pybedtools/include/bedFile.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include
copying pybedtools/include/fileType.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include
copying pybedtools/include/fileType.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include
copying pybedtools/include/gzstream.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include
copying pybedtools/include/gzstream.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include
copying pybedtools/test/data/small.fastq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/b.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/x.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/d.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/x.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/small.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/c.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/y.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/mpl-expected.png -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_cases.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
creating build/temp.linux-aarch64-cpython-312
creating build/temp.linux-aarch64-cpython-312/pybedtools
creating build/temp.linux-aarch64-cpython-312/pybedtools/include
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/cbedtools.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/pybedtools/cbedtools.o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/aarch64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/cbedtools.cpython-312-aarch64-linux-gnu.so
building 'pybedtools.featurefuncs' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/featurefuncs.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/pybedtools/featurefuncs.o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/aarch64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/featurefuncs.cpython-312-aarch64-linux-gnu.so
python3 setup.py develop --user
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running develop
/usr/lib/python3/dist-packages/setuptools/command/develop.py:41: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  easy_install.initialize_options(self)
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
running egg_info
writing pybedtools.egg-info/PKG-INFO
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pybedtools'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
running build_ext
building 'pybedtools.cbedtools' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/cbedtools.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/pybedtools/cbedtools.o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/aarch64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/pybedtools/cbedtools.cpython-312-aarch64-linux-gnu.so
building 'pybedtools.featurefuncs' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/featurefuncs.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/pybedtools/featurefuncs.o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/aarch64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/pybedtools/featurefuncs.cpython-312-aarch64-linux-gnu.so
Creating /<<PKGBUILDDIR>>/fakehome/.local/lib/python3.12/site-packages/pybedtools.egg-link (link to .)
Adding pybedtools 0.10.0 to easy-install.pth file

Installed /<<PKGBUILDDIR>>
Processing dependencies for pybedtools==0.10.0
Searching for pysam==0.22.1
Best match: pysam 0.22.1
Adding pysam 0.22.1 to easy-install.pth file

Using /usr/lib/python3/dist-packages
Searching for numpy==1.26.4
Best match: numpy 1.26.4
Adding numpy 1.26.4 to easy-install.pth file
Installing f2py script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing f2py3 script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing f2py3.13 script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing f2py3.12 script to /<<PKGBUILDDIR>>/fakehome/.local/bin

Using /usr/lib/python3/dist-packages
Finished processing dependencies for pybedtools==0.10.0
sphinx-build -N -b html docs/source docs/html
Running Sphinx v7.4.7
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
[autosummary] generating autosummary for: /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst, /<<PKGBUILDDIR>>/docs/source/pybedtools.featurefuncs.add_color.rst, /<<PKGBUILDDIR>>/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst, /<<PKGBUILDDIR>>/docs/source/pybedtools.featurefuncs.extend_fields.rst, /<<PKGBUILDDIR>>/docs/source/pybedtools.featurefuncs.five_prime.rst, /<<PKGBUILDDIR>>/docs/source/pybedtools.featurefuncs.greater_than.rst, /<<PKGBUILDDIR>>/docs/source/pybedtools.featurefuncs.less_than.rst, /<<PKGBUILDDIR>>/docs/source/pybedtools.featurefuncs.normalized_to_length.rst, /<<PKGBUILDDIR>>/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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  warn(msg)
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: Unknown section Example in the docstring of tag_bedpe in /<<PKGBUILDDIR>>/pybedtools/contrib/long_range_interaction.py.
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reading sources... [ 96%] topical-documentation-contents
reading sources... [ 96%] topical-genome
reading sources... [ 97%] topical-iterators
reading sources... [ 97%] topical-low-level-ops
reading sources... [ 98%] topical-random
reading sources... [ 99%] topical-saving
reading sources... [ 99%] topical-wrapping
reading sources... [100%] tutorial-contents

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/<<PKGBUILDDIR>>/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy<https://github.com/vanheeringen-lab/genomepy/>".
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/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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.
/<<PKGBUILDDIR>>/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: '$'. Retrying in relaxed mode.
/<<PKGBUILDDIR>>/docs/source/default-arguments.rst:35: WARNING: Lexing literal_block '$ intersectBed -a a.bed -b b.bed -u > tmpfile' as "python" resulted in an error at token: '$'. Retrying in relaxed mode.
/<<PKGBUILDDIR>>/docs/source/topical-design-principles.rst:120: WARNING: unknown option: 'mergeBed -i'
/<<PKGBUILDDIR>>/docs/source/topical-design-principles.rst:127: WARNING: unknown option: '-i'
generating indices... genindex py-modindex done
highlighting module code... [  8%] pybedtools
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highlighting module code... [ 85%] pybedtools.filenames
highlighting module code... [ 92%] pybedtools.helpers
highlighting module code... [100%] pybedtools.parallel

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

The HTML pages are in docs/html.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -a -O--buildsystem=pybuild
I: pybuild pybuild:308: cp /<<PKGBUILDDIR>>/debian/mpl-expected.png /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/ ; python3 /<<PKGBUILDDIR>>/setup.py install --user ; export HOME=/<<PKGBUILDDIR>>/fakehome
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  self.initialize_options()
running bdist_egg
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'
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adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-aarch64/egg
running install_lib
running build_py
creating build/lib.linux-aarch64-cpython-312
creating build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/helpers.py -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/logger.py -> build/lib.linux-aarch64-cpython-312/pybedtools
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copying pybedtools/stats.py -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/settings.py -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/paths.py -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/version.py -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/__init__.py -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-aarch64-cpython-312/pybedtools
creating build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_contrib.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/regression_tests.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_1.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_helpers.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_len_leak.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/__init__.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_issues.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test
creating build/lib.linux-aarch64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-aarch64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-aarch64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-aarch64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-aarch64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-aarch64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-aarch64-cpython-312/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-aarch64-cpython-312/pybedtools/contrib
creating build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _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-aarch64-cpython-312/pybedtools
copying pybedtools/cbedtools.cpp -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/featurefuncs.cpp -> build/lib.linux-aarch64-cpython-312/pybedtools
copying pybedtools/featurefuncs.pyx -> build/lib.linux-aarch64-cpython-312/pybedtools
creating build/lib.linux-aarch64-cpython-312/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-aarch64-cpython-312/pybedtools/include
copying pybedtools/include/bedFile.h -> build/lib.linux-aarch64-cpython-312/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-aarch64-cpython-312/pybedtools/include
copying pybedtools/include/fileType.h -> build/lib.linux-aarch64-cpython-312/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-aarch64-cpython-312/pybedtools/include
copying pybedtools/include/gzstream.h -> build/lib.linux-aarch64-cpython-312/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-aarch64-cpython-312/pybedtools/include
copying pybedtools/test/data/small.fastq -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/b.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test.fa -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/x.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-aarch64-cpython-312/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/mpl-expected.png -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_cases.yaml -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-aarch64-cpython-312/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-aarch64-cpython-312/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/cbedtools.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/pybedtools/cbedtools.o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/aarch64-linux-gnu -lstdc++ -lz -o build/lib.linux-aarch64-cpython-312/pybedtools/cbedtools.cpython-312-aarch64-linux-gnu.so
building 'pybedtools.featurefuncs' extension
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/featurefuncs.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o
aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-312/pybedtools/featurefuncs.o build/temp.linux-aarch64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-312/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/aarch64-linux-gnu -lstdc++ -lz -o build/lib.linux-aarch64-cpython-312/pybedtools/featurefuncs.cpython-312-aarch64-linux-gnu.so
creating build/bdist.linux-aarch64
creating build/bdist.linux-aarch64/egg
creating build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/helpers.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/cbedtools.pxd -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/genome_registry.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/cbedtools.pyx -> build/bdist.linux-aarch64/egg/pybedtools
creating build/bdist.linux-aarch64/egg/pybedtools/include
copying build/lib.linux-aarch64-cpython-312/pybedtools/include/bedFile.cpp -> build/bdist.linux-aarch64/egg/pybedtools/include
copying build/lib.linux-aarch64-cpython-312/pybedtools/include/fileType.cpp -> build/bdist.linux-aarch64/egg/pybedtools/include
copying build/lib.linux-aarch64-cpython-312/pybedtools/include/gzstream.cpp -> build/bdist.linux-aarch64/egg/pybedtools/include
copying build/lib.linux-aarch64-cpython-312/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-aarch64/egg/pybedtools/include
copying build/lib.linux-aarch64-cpython-312/pybedtools/include/fileType.h -> build/bdist.linux-aarch64/egg/pybedtools/include
copying build/lib.linux-aarch64-cpython-312/pybedtools/include/bedFile.h -> build/bdist.linux-aarch64/egg/pybedtools/include
copying build/lib.linux-aarch64-cpython-312/pybedtools/include/gzstream.h -> build/bdist.linux-aarch64/egg/pybedtools/include
copying build/lib.linux-aarch64-cpython-312/pybedtools/filenames.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/logger.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/parallel.py -> build/bdist.linux-aarch64/egg/pybedtools
creating build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_contrib.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_pathlib.py -> build/bdist.linux-aarch64/egg/pybedtools/test
creating build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/small.fastq -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/b.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.gff -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/genome.fa -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/m1.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/x.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/v.vcf -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/test.fa -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/venn.c.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/d.gff -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/x.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/issue319.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/reads.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/a.igv_script -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/issue_121.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/hg19.gff -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.cram -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/small.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/venn.b.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/bedpe.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/a.links.html -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/exons.gff -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/__init__.py -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/a.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/test.fa.fai -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/expand_test.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/164.gtf -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/c.gff -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/data/y.bam -> build/bdist.linux-aarch64/egg/pybedtools/test/data
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_cases.yaml -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/genomepy_integration.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_merge227.yaml -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/mpl-expected.png -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/gchart-expected.png -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_iter.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/regression_tests.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_cbedtools.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_1.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_helpers.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_merge215.yaml -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_len_leak.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/__init__.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_issues.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/tfuncs.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/test/test_gzip_support.py -> build/bdist.linux-aarch64/egg/pybedtools/test
copying build/lib.linux-aarch64-cpython-312/pybedtools/cbedtools.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/pybedtools
creating build/bdist.linux-aarch64/egg/pybedtools/contrib
copying build/lib.linux-aarch64-cpython-312/pybedtools/contrib/venn_maker.py -> build/bdist.linux-aarch64/egg/pybedtools/contrib
copying build/lib.linux-aarch64-cpython-312/pybedtools/contrib/plotting.py -> build/bdist.linux-aarch64/egg/pybedtools/contrib
copying build/lib.linux-aarch64-cpython-312/pybedtools/contrib/bigwig.py -> build/bdist.linux-aarch64/egg/pybedtools/contrib
copying build/lib.linux-aarch64-cpython-312/pybedtools/contrib/bigbed.py -> build/bdist.linux-aarch64/egg/pybedtools/contrib
copying build/lib.linux-aarch64-cpython-312/pybedtools/contrib/__init__.py -> build/bdist.linux-aarch64/egg/pybedtools/contrib
copying build/lib.linux-aarch64-cpython-312/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-aarch64/egg/pybedtools/contrib
copying build/lib.linux-aarch64-cpython-312/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-aarch64/egg/pybedtools/contrib
copying build/lib.linux-aarch64-cpython-312/pybedtools/stats.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/settings.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/paths.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/version.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/featurefuncs.pyx -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/__init__.py -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/featurefuncs.cpp -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/_Window.pyx -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/cbedtools.cpp -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/featurefuncs.cpython-312-aarch64-linux-gnu.so -> build/bdist.linux-aarch64/egg/pybedtools
copying build/lib.linux-aarch64-cpython-312/pybedtools/bedtool.py -> build/bdist.linux-aarch64/egg/pybedtools
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/helpers.py to helpers.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/genome_registry.py to genome_registry.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/filenames.py to filenames.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/logger.py to logger.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/parallel.py to parallel.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_contrib.py to test_contrib.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_pathlib.py to test_pathlib.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/data/__init__.py to __init__.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/genomepy_integration.py to genomepy_integration.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_iter.py to test_iter.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/regression_tests.py to regression_tests.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_cbedtools.py to test_cbedtools.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_1.py to test_1.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_helpers.py to test_helpers.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_len_leak.py to test_len_leak.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/__init__.py to __init__.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_issues.py to test_issues.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/tfuncs.py to tfuncs.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/test/test_gzip_support.py to test_gzip_support.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/contrib/venn_maker.py to venn_maker.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/contrib/plotting.py to plotting.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/contrib/bigwig.py to bigwig.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/contrib/bigbed.py to bigbed.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/contrib/__init__.py to __init__.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/contrib/long_range_interaction.py to long_range_interaction.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/contrib/intersection_matrix.py to intersection_matrix.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/stats.py to stats.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/settings.py to settings.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/paths.py to paths.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/version.py to version.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/__init__.py to __init__.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/bedtool.py to bedtool.cpython-312.pyc
creating stub loader for pybedtools/cbedtools.cpython-312-aarch64-linux-gnu.so
creating stub loader for pybedtools/featurefuncs.cpython-312-aarch64-linux-gnu.so
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/cbedtools.py to cbedtools.cpython-312.pyc
byte-compiling build/bdist.linux-aarch64/egg/pybedtools/featurefuncs.py to featurefuncs.cpython-312.pyc
creating build/bdist.linux-aarch64/egg/EGG-INFO
copying pybedtools.egg-info/PKG-INFO -> build/bdist.linux-aarch64/egg/EGG-INFO
copying pybedtools.egg-info/SOURCES.txt -> build/bdist.linux-aarch64/egg/EGG-INFO
copying pybedtools.egg-info/dependency_links.txt -> build/bdist.linux-aarch64/egg/EGG-INFO
copying pybedtools.egg-info/not-zip-safe -> build/bdist.linux-aarch64/egg/EGG-INFO
copying pybedtools.egg-info/requires.txt -> build/bdist.linux-aarch64/egg/EGG-INFO
copying pybedtools.egg-info/top_level.txt -> build/bdist.linux-aarch64/egg/EGG-INFO
writing build/bdist.linux-aarch64/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/pybedtools-0.10.0-py3.12-linux-aarch64.egg' and adding 'build/bdist.linux-aarch64/egg' to it
removing 'build/bdist.linux-aarch64/egg' (and everything under it)
Processing pybedtools-0.10.0-py3.12-linux-aarch64.egg
creating /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/lib/python3.12/site-packages/pybedtools-0.10.0-py3.12-linux-aarch64.egg
Extracting pybedtools-0.10.0-py3.12-linux-aarch64.egg to /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/lib/python3.12/site-packages
Adding pybedtools 0.10.0 to easy-install.pth file

Installed /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/lib/python3.12/site-packages/pybedtools-0.10.0-py3.12-linux-aarch64.egg
Processing dependencies for pybedtools==0.10.0
Searching for pysam==0.22.1
Best match: pysam 0.22.1
Adding pysam 0.22.1 to easy-install.pth file
detected new path './pybedtools-0.10.0-py3.12-linux-aarch64.egg'

Using /usr/lib/python3/dist-packages
Searching for numpy==1.26.4
Best match: numpy 1.26.4
Adding numpy 1.26.4 to easy-install.pth file
Installing f2py script to /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/bin
Installing f2py3 script to /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/bin
Installing f2py3.13 script to /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/bin
Installing f2py3.12 script to /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/bin

Using /usr/lib/python3/dist-packages
Finished processing dependencies for pybedtools==0.10.0
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build; python3.13 -m pytest -k "not test_chromsizes"
============================= test session starts ==============================
platform linux -- Python 3.13.0rc3, pytest-8.3.3, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build
configfile: pyproject.toml
plugins: typeguard-4.3.0
collected 511 items / 2 deselected / 509 selected

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

=================================== FAILURES ===================================
________________________________ test_issue_405 ________________________________

self = <BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>
others = (PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'),)
kwargs = {}
other_beds = [<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'))>]
other = <BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'))>
postmerge = True, force_truncate = False, stream_merge = False

    @_log_to_history
    def cat(self, *others, **kwargs):
        """
        Concatenate interval files together.
    
        Concatenates two BedTool objects (or an object and a file) and does an
        optional post-merge of the features.
    
        *postmerge=True* by default; use *postmerge=False* if you want to keep
        features separate.
    
        *force_truncate=False* by default; *force_truncate=True* to truncate
        all files to chrom, start, stop.
    
        When *force_truncate=False* and *postmerge=False*, the output will
        contain the smallest number of fields observed across all inputs. This
        maintains compatibility with BEDTools programs, which assume constant
        number of fields in all lines of a file.
    
        Other kwargs are sent to :meth:`BedTool.merge` (and assuming that
        *postmerge=True*).
    
        Example usage:
    
        >>> a = pybedtools.example_bedtool('a.bed')
        >>> b = pybedtools.example_bedtool('b.bed')
        >>> print(a.cat(b)) #doctest: +NORMALIZE_WHITESPACE
        chr1	1	500
        chr1	800	950
        <BLANKLINE>
        >>> print(a.cat(*[b,b],
        ...   postmerge=False)) #doctest: +NORMALIZE_WHITESPACE
        chr1	1	100	feature1	0	+
        chr1	100	200	feature2	0	+
        chr1	150	500	feature3	0	-
        chr1	900	950	feature4	0	+
        chr1	155	200	feature5	0	-
        chr1	800	901	feature6	0	+
        chr1	155	200	feature5	0	-
        chr1	800	901	feature6	0	+
        <BLANKLINE>
        """
        assert len(others) > 0, "You must specify at least one other bedfile!"
        other_beds = []
        for other in others:
            if isinstance(other, (str, Path)):
                other = BedTool(other)
            else:
                assert isinstance(
                    other, BedTool
                ), "Either filename or another BedTool instance required"
            other_beds.append(other)
    
        # postmerge and force_trucate don't get passed on to merge
        postmerge = kwargs.pop("postmerge", True)
        force_truncate = kwargs.pop("force_truncate", False)
        stream_merge = kwargs.get("stream", False)
        if stream_merge and postmerge:
            raise ValueError(
                "The post-merge step in the `cat()` method "
                "perfoms a sort, which uses stream=True.  Using "
                "stream=True for the merge as well will result in a "
                "deadlock!"
            )
    
        # if filetypes and field counts are the same, don't truncate
        if not force_truncate:
            try:
>               a_type = self.file_type

pybedtools/bedtool.py:3240: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>

    @property
    def file_type(self):
        """
        Return the type of the current file.  One of ('bed','vcf','gff', 'bam',
        'sam', 'empty').
    
        >>> a = pybedtools.example_bedtool('a.bed')
        >>> print(a.file_type)
        bed
        """
        if not isinstance(self.fn, str):
>           raise ValueError(
                "Checking file_type not supported for "
                "non-file BedTools. Use .saveas() to "
                "save as a temp file first."
            )
E           ValueError: Checking file_type not supported for non-file BedTools. Use .saveas() to save as a temp file first.

pybedtools/bedtool.py:1106: ValueError

During handling of the above exception, another exception occurred:

    def test_issue_405():
        a = Path(pybedtools.example_filename('a.bed'))
        b = Path(pybedtools.example_filename('b.bed'))
        a = pybedtools.BedTool(a)
>       a.cat(b)

pybedtools/test/test_issues.py:921: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
pybedtools/bedtool.py:907: in decorated
    result = method(self, *args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>
others = (PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'),)
kwargs = {}
other_beds = [<BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'))>]
other = <BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed'))>
postmerge = True, force_truncate = False, stream_merge = False

    @_log_to_history
    def cat(self, *others, **kwargs):
        """
        Concatenate interval files together.
    
        Concatenates two BedTool objects (or an object and a file) and does an
        optional post-merge of the features.
    
        *postmerge=True* by default; use *postmerge=False* if you want to keep
        features separate.
    
        *force_truncate=False* by default; *force_truncate=True* to truncate
        all files to chrom, start, stop.
    
        When *force_truncate=False* and *postmerge=False*, the output will
        contain the smallest number of fields observed across all inputs. This
        maintains compatibility with BEDTools programs, which assume constant
        number of fields in all lines of a file.
    
        Other kwargs are sent to :meth:`BedTool.merge` (and assuming that
        *postmerge=True*).
    
        Example usage:
    
        >>> a = pybedtools.example_bedtool('a.bed')
        >>> b = pybedtools.example_bedtool('b.bed')
        >>> print(a.cat(b)) #doctest: +NORMALIZE_WHITESPACE
        chr1	1	500
        chr1	800	950
        <BLANKLINE>
        >>> print(a.cat(*[b,b],
        ...   postmerge=False)) #doctest: +NORMALIZE_WHITESPACE
        chr1	1	100	feature1	0	+
        chr1	100	200	feature2	0	+
        chr1	150	500	feature3	0	-
        chr1	900	950	feature4	0	+
        chr1	155	200	feature5	0	-
        chr1	800	901	feature6	0	+
        chr1	155	200	feature5	0	-
        chr1	800	901	feature6	0	+
        <BLANKLINE>
        """
        assert len(others) > 0, "You must specify at least one other bedfile!"
        other_beds = []
        for other in others:
            if isinstance(other, (str, Path)):
                other = BedTool(other)
            else:
                assert isinstance(
                    other, BedTool
                ), "Either filename or another BedTool instance required"
            other_beds.append(other)
    
        # postmerge and force_trucate don't get passed on to merge
        postmerge = kwargs.pop("postmerge", True)
        force_truncate = kwargs.pop("force_truncate", False)
        stream_merge = kwargs.get("stream", False)
        if stream_merge and postmerge:
            raise ValueError(
                "The post-merge step in the `cat()` method "
                "perfoms a sort, which uses stream=True.  Using "
                "stream=True for the merge as well will result in a "
                "deadlock!"
            )
    
        # if filetypes and field counts are the same, don't truncate
        if not force_truncate:
            try:
                a_type = self.file_type
    
                files = [self] + other_beds
                filetypes = set(
                    [self.file_type] + [i.file_type for i in other_beds]
                ).difference(["empty"])
                field_nums = (
                    set([self.field_count()] + [i.field_count() for i in other_beds])
                    .difference([None])
                    .difference([0])
                )
                same_field_num = len(field_nums) == 1
                same_type = len(set(filetypes)) == 1
            except ValueError:
>               raise ValueError(
                    "Can't check filetype or field count -- "
                    "is one of the files you're merging a 'streaming' "
                    "BedTool?  If so, use .saveas() to save to file first"
                )
E               ValueError: Can't check filetype or field count -- is one of the files you're merging a 'streaming' BedTool?  If so, use .saveas() to save to file first

pybedtools/bedtool.py:3254: ValueError
______________________________ test_pathlib_base _______________________________

    def test_pathlib_base():
        file = "a.bed"
        fn = os.path.join(pybedtools.filenames.data_dir(), file)
        path = pathlib.PurePath(fn)
>       assert pybedtools.BedTool(path).fn == fn
E       AssertionError: assert PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed') == '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'
E        +  where PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed') = <BedTool(PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>.fn
E        +    where <BedTool(PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))> = <class 'pybedtools.bedtool.BedTool'>(PurePosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))
E        +      where <class 'pybedtools.bedtool.BedTool'> = pybedtools.BedTool

pybedtools/test/test_pathlib.py:12: AssertionError
_____________________________ test_pathlib_derived _____________________________

    def test_pathlib_derived():
        file = "a.bed"
        fn = os.path.join(pybedtools.filenames.data_dir(), file)
        path = pathlib.Path(fn)
>       assert pybedtools.BedTool(path).fn == fn
E       AssertionError: assert PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed') == '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'
E        +  where PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed') = <BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))>.fn
E        +    where <BedTool(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))> = <class 'pybedtools.bedtool.BedTool'>(PosixPath('/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed'))
E        +      where <class 'pybedtools.bedtool.BedTool'> = pybedtools.BedTool

pybedtools/test/test_pathlib.py:19: AssertionError
________________________ test_pathlib_nonexistent_file _________________________

    def test_pathlib_nonexistent_file():
        fn = os.path.join(pybedtools.filenames.data_dir(), "this_file_is_missing")
        path = pathlib.Path(fn)
>       with pytest.raises(FileNotFoundError):
E       Failed: DID NOT RAISE <class 'FileNotFoundError'>

pybedtools/test/test_pathlib.py:26: Failed
=========================== short test summary info ============================
FAILED pybedtools/test/test_issues.py::test_issue_405 - ValueError: Can't che...
FAILED pybedtools/test/test_pathlib.py::test_pathlib_base - AssertionError: a...
FAILED pybedtools/test/test_pathlib.py::test_pathlib_derived - AssertionError...
FAILED pybedtools/test/test_pathlib.py::test_pathlib_nonexistent_file - Faile...
=========== 4 failed, 502 passed, 2 deselected, 3 xfailed in 18.47s ============
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build; python3.13 -m pytest -k "not test_chromsizes"
I: pybuild pybuild:308: cp /<<PKGBUILDDIR>>/debian/mpl-expected.png /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/ ; python3 /<<PKGBUILDDIR>>/setup.py install --user ; export HOME=/<<PKGBUILDDIR>>/fakehome
/<<PKGBUILDDIR>>/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
  warnings.warn(msg)
running install
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
error: can't combine user with prefix, exec_prefix/home, or install_(plat)base
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build; python3.12 -m pytest -k "not test_chromsizes"
============================= test session starts ==============================
platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pybedtools/build
configfile: pyproject.toml
plugins: typeguard-4.3.0
collected 511 items / 2 deselected / 509 selected

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

================ 506 passed, 2 deselected, 3 xfailed in 18.70s =================
I: pybuild pybuild:334: cd /<<PKGBUILDDIR>>/docs ; make clean doctest
make[1]: Entering directory '/<<PKGBUILDDIR>>/docs'
rm -rf build/* source/autodocs/*.rst
sphinx-build -b doctest -d build/doctrees   source build/doctest
Running Sphinx v7.4.7
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
[autosummary] generating autosummary for: /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.filenames.example_filename.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.filenames.list_example_files.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.chromsizes.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.chromsizes_to_file.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.cleanup.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.get_chromsizes_from_ucsc.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.get_tempdir.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.set_bedtools_path.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst
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building [doctest]: targets for 48 source files that are out of date
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  warn(msg)
/usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: Unknown section Example in the docstring of tag_bedpe in /<<PKGBUILDDIR>>/pybedtools/contrib/long_range_interaction.py.
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reading sources... [ 94%] topical-comparisons
reading sources... [ 94%] topical-create-a-bedtool
reading sources... [ 95%] topical-design-principles
reading sources... [ 96%] topical-documentation-contents
reading sources... [ 96%] topical-genome
reading sources... [ 97%] topical-iterators
reading sources... [ 97%] topical-low-level-ops
reading sources... [ 98%] topical-random
reading sources... [ 99%] topical-saving
reading sources... [ 99%] topical-wrapping
reading sources... [100%] tutorial-contents

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Doctest summary
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Testing of doctests in the sources finished, look at the results in build/doctest/output.txt.
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make[1]: Leaving directory '/<<PKGBUILDDIR>>/docs'
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| Summary                                                                      |
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Build Architecture: arm64
Build Type: any
Build-Space: 156528
Build-Time: 180
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 119
Job: /tmp/debusine-fetch-exec-upload-hrwtdgq0/python-pybedtools_0.10.0-1.dsc
Machine Architecture: arm64
Package: python-pybedtools
Package-Time: 343
Source-Version: 0.10.0-1
Space: 156528
Status: attempted
Version: 0.10.0-1+bd1
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Finished at 2024-10-07T01:44:22Z
Build needed 00:05:43, 156528k disk space

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