python-pybedtools →
0.9.1-1 →
armhf → 2023-11-06 05:10:01
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| python-pybedtools 0.9.1-1 (armhf) Mon, 06 Nov 2023 05:04:40 +0000 |
+==============================================================================+
Package: python-pybedtools
Version: 0.9.1-1
Source Version: 0.9.1-1
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-8c77828a-7aad-4906-b553-5ae8da9f5c49' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/python-pybedtools-pNVMlc/resolver-eyWQ1W' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.2 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [14.9 MB]
Fetched 29.1 MB in 5s (5478 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'python-pybedtools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/python-pybedtools.git
Please use:
git clone https://salsa.debian.org/med-team/python-pybedtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 12.1 MB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main python-pybedtools 0.9.1-1 (dsc) [2520 B]
Get:2 http://172.17.4.1/private trixie-staging/main python-pybedtools 0.9.1-1 (tar) [12.0 MB]
Get:3 http://172.17.4.1/private trixie-staging/main python-pybedtools 0.9.1-1 (diff) [29.9 kB]
Fetched 12.1 MB in 1s (8321 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/python-pybedtools-pNVMlc/python-pybedtools-0.9.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/python-pybedtools-pNVMlc' 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
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
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [877 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [909 B]
Fetched 2395 B in 0s (0 B/s)
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 bsdextrautils
ca-certificates cython3 debhelper dh-autoreconf dh-python
dh-strip-nondeterminism docutils-common dpkg-dev dwz file fontconfig
fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblas3
libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1
libdebhelper-perl libdeflate0 libdpkg-perl libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2
libice6 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery
libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl liblapack3
liblbfgsb0 liblcms2-2 liblerc4 libmagic-mgc libmagic1 libnghttp2-14
libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpsl5
libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11
libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0
libraqm0 librtmp1 libsharpyuv0 libsm6 libssh2-1 libsub-override-perl
libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool libuchardet0
libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
libxrender1 libxslt1.1 libxss1 libxt6 libyaml-0-2 m4 man-db media-types
openssl po-debconf python-babel-localedata python-matplotlib-data python3
python3-alabaster python3-all python3-all-dev python3-appdirs python3-attr
python3-babel python3-brotli python3-certifi python3-chardet
python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil
python3-decorator python3-dev python3-distutils python3-docutils
python3-fonttools python3-fs python3-idna python3-imagesize
python3-iniconfig python3-jinja2 python3-kiwisolver python3-lib2to3
python3-lxml python3-lz4 python3-markupsafe python3-matplotlib
python3-minimal 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-tk python3-tz
python3-ufolib2 python3-urllib3 python3-yaml python3.11 python3.11-dev
python3.11-minimal r-base-core sensible-utils sgml-base sphinx-common
tk8.6-blt2.5 ucf unicode-data unzip x11-common xdg-utils xml-core zip
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc blt-demo cython-doc dh-make flit
python3-build python3-installer python3-wheel debian-keyring gettext-doc
libasprintf-dev libgettextpo-dev groff git bzr low-memory-monitor
libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
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 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-pandas-doc python3-statsmodels python-pil-doc
python-psutil-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
fonts-freefont-otf imagemagick-6.q16 latexmk libjs-mathjax
python3-sphinx-rtd-theme sphinx-doc tex-gyre texlive-fonts-recommended
texlive-plain-generic texlive-fonts-extra python-sympy-doc tix
python3-tk-dbg python3.11-venv python3.11-doc binfmt-support elpa-ess
r-doc-info | r-doc-pdf r-mathlib r-base-html sgml-base-doc
Recommended packages:
libalgorithm-merge-perl curl | wget | lynx libfile-fcntllock-perl
libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs
javascript-common libjson-xs-perl publicsuffix libltdl-dev
libmail-sendmail-perl python3-bs4 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 bsdextrautils
ca-certificates cython3 debhelper dh-autoreconf dh-python
dh-strip-nondeterminism docutils-common dwz file fontconfig
fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libblas3
libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1
libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2
libice6 libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery
libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-perl liblapack3
liblbfgsb0 liblcms2-2 liblerc4 libmagic-mgc libmagic1 libnghttp2-14
libopenjp2-7 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng16-16 libpsl5
libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11
libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0
libraqm0 librtmp1 libsharpyuv0 libsm6 libssh2-1 libsub-override-perl
libtcl8.6 libthai-data libthai0 libtiff6 libtk8.6 libtool libuchardet0
libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
libxrender1 libxslt1.1 libxss1 libxt6 libyaml-0-2 m4 man-db media-types
openssl po-debconf python-babel-localedata python-matplotlib-data python3
python3-alabaster python3-all python3-all-dev python3-appdirs python3-attr
python3-babel python3-brotli python3-certifi python3-chardet
python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil
python3-decorator python3-dev python3-distutils python3-docutils
python3-fonttools python3-fs python3-idna python3-imagesize
python3-iniconfig python3-jinja2 python3-kiwisolver python3-lib2to3
python3-lxml python3-lz4 python3-markupsafe python3-matplotlib
python3-minimal 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-tk python3-tz
python3-ufolib2 python3-urllib3 python3-yaml python3.11 python3.11-dev
python3.11-minimal r-base-core sbuild-build-depends-main-dummy
sensible-utils sgml-base sphinx-common tk8.6-blt2.5 ucf unicode-data unzip
x11-common xdg-utils xml-core zip zlib1g-dev
The following packages will be upgraded:
dpkg-dev libdpkg-perl
2 upgraded, 197 newly installed, 0 to remove and 8 not upgraded.
1 not fully installed or removed.
Need to get 142 MB/144 MB of archives.
After this operation, 528 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [984 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.6-3 [800 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.6-3 [1674 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.6-3 [1679 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.6-3 [586 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:10 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf sgml-base all 1.31 [15.4 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-5 [80.8 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.11.2-3 [1342 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf openssl armhf 3.0.11-1 [1367 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf ca-certificates all 20230311 [153 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-13 [156 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf ucf all 3.0043+nmu1 [55.2 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-13 [496 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf bedtools armhf 2.31.0+dfsg-1 [508 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libtcl8.6 armhf 8.6.13+dfsg-2 [904 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.0.9-2+b3 [258 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libpng16-16 armhf 1.6.40-2 [258 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libfreetype6 armhf 2.13.2+dfsg-1 [366 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-mono all 2.37-8 [489 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf fonts-dejavu-core all 2.37-8 [840 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf fontconfig-config armhf 2.14.2-6 [316 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libfontconfig1 armhf 2.14.2-6 [367 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libbsd0 armhf 0.11.7-4 [111 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libxcb1 armhf 1.15-1 [139 kB]
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Get:44 http://172.17.4.1/private trixie-staging/main armhf libx11-6 armhf 2:1.8.7-1 [729 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libxrender1 armhf 1:0.9.10-1.1 [30.0 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libxft2 armhf 2.3.6-1 [53.7 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libtk8.6 armhf 8.6.13-2 [680 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf tk8.6-blt2.5 armhf 2.5.3+dfsg-4.1 [477 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf blt armhf 2.5.3+dfsg-4.1 [14.9 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf cython3 armhf 0.29.36-1 [1212 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.7 [82.1 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-13 [1201 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.7 [956 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf python3-distutils all 3.11.5-1 [131 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf python3-pkg-resources all 68.1.2-2 [241 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf python3-setuptools all 68.1.2-2 [468 kB]
Get:73 http://172.17.4.1/private trixie-staging/main armhf dh-python all 6.20231025 [107 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf docutils-common all 0.19+dfsg-8 [127 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf fontconfig armhf 2.14.2-6 [461 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf fonts-lyx all 2.3.7-1 [186 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libblas3 armhf 3.11.0-2 [100.0 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libpixman-1-0 armhf 0.42.2-1 [461 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libxcb-render0 armhf 1.15-1 [114 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libxcb-shm0 armhf 1.15-1 [106 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libcairo2 armhf 1.18.0-1 [425 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.57.0-1 [61.6 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-2 [195 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.4.0-2+rpi1 [358 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 8.4.0-2+rpi1 [362 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libdatrie1 armhf 0.2.13-2+b2 [39.9 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libexpat1-dev armhf 2.5.0-2 [130 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libfribidi0 armhf 1.0.13-3 [69.9 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-5+rpi1 [247 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libglib2.0-0 armhf 2.78.0-2+rpi1 [1249 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf libharfbuzz0b armhf 8.0.1-1 [2098 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.5.2-1 [60.0 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.17+ds-1 [374 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libimagequant0 armhf 2.17.0-1 [28.0 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libjbig0 armhf 2.1-6.1 [27.0 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf libjs-sphinxdoc all 5.3.0-7 [131 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libjson-perl all 4.10000-1 [87.5 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf liblapack3 armhf 3.11.0-2 [1624 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf liblbfgsb0 armhf 3.0+dfsg.4-1 [24.4 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf liblcms2-2 armhf 2.14-2 [124 kB]
Get:111 http://172.17.4.1/private trixie-staging/main armhf liblerc4 armhf 4.0.0+ds-3 [133 kB]
Get:112 http://172.17.4.1/private trixie-staging/main armhf libopenjp2-7 armhf 2.5.0-2 [164 kB]
Get:113 http://172.17.4.1/private trixie-staging/main armhf libthai-data all 0.1.29-1 [176 kB]
Get:114 http://172.17.4.1/private trixie-staging/main armhf libthai0 armhf 0.1.29-1 [54.5 kB]
Get:115 http://172.17.4.1/private trixie-staging/main armhf libpango-1.0-0 armhf 1.51.0+ds-2 [187 kB]
Get:116 http://172.17.4.1/private trixie-staging/main armhf libpangoft2-1.0-0 armhf 1.51.0+ds-2 [40.4 kB]
Get:117 http://172.17.4.1/private trixie-staging/main armhf libpangocairo-1.0-0 armhf 1.51.0+ds-2 [30.0 kB]
Get:118 http://172.17.4.1/private trixie-staging/main armhf libpaper1 armhf 1.1.29 [11.9 kB]
Get:119 http://172.17.4.1/private trixie-staging/main armhf libpaper-utils armhf 1.1.29 [8416 B]
Get:120 http://172.17.4.1/private trixie-staging/main armhf libpython3.11 armhf 3.11.6-3 [1662 kB]
Get:121 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:122 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-dev armhf 3.11.6-3 [3271 kB]
Get:123 http://172.17.4.1/private trixie-staging/main armhf libpython3-dev armhf 3.11.4-5 [9432 B]
Get:124 http://172.17.4.1/private trixie-staging/main armhf libpython3-all-dev armhf 3.11.4-5 [1068 B]
Get:125 http://172.17.4.1/private trixie-staging/main armhf libqhull-r8.0 armhf 2020.2-6 [216 kB]
Get:126 http://172.17.4.1/private trixie-staging/main armhf libraqm0 armhf 0.10.1-1 [11.7 kB]
Get:127 http://172.17.4.1/private trixie-staging/main armhf libsharpyuv0 armhf 1.3.2-0.3 [106 kB]
Get:128 http://172.17.4.1/private trixie-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:129 http://172.17.4.1/private trixie-staging/main armhf libwebp7 armhf 1.3.2-0.3 [261 kB]
Get:130 http://172.17.4.1/private trixie-staging/main armhf libtiff6 armhf 4.5.1+git230720-1 [298 kB]
Get:131 http://172.17.4.1/private trixie-staging/main armhf libwebpdemux2 armhf 1.3.2-0.3 [106 kB]
Get:132 http://172.17.4.1/private trixie-staging/main armhf libwebpmux3 armhf 1.3.2-0.3 [116 kB]
Get:133 http://172.17.4.1/private trixie-staging/main armhf libxslt1.1 armhf 1.1.35-1 [221 kB]
Get:134 http://172.17.4.1/private trixie-staging/main armhf libxt6 armhf 1:1.2.1-1.1 [155 kB]
Get:135 http://172.17.4.1/private trixie-staging/main armhf libyaml-0-2 armhf 0.2.5-1 [44.6 kB]
Get:136 http://172.17.4.1/private trixie-staging/main armhf python-babel-localedata all 2.10.3-2 [5611 kB]
Get:137 http://172.17.4.1/private trixie-staging/main armhf python-matplotlib-data all 3.6.3-1 [2744 kB]
Get:138 http://172.17.4.1/private trixie-staging/main armhf python3-alabaster all 0.7.12-1 [20.8 kB]
Get:139 http://172.17.4.1/private trixie-staging/main armhf python3-all armhf 3.11.4-5 [1060 B]
Get:140 http://172.17.4.1/private trixie-staging/main armhf python3.11-dev armhf 3.11.6-3 [508 kB]
Get:141 http://172.17.4.1/private trixie-staging/main armhf python3-dev armhf 3.11.4-5 [26.2 kB]
Get:142 http://172.17.4.1/private trixie-staging/main armhf python3-all-dev armhf 3.11.4-5 [1068 B]
Get:143 http://172.17.4.1/private trixie-staging/main armhf python3-appdirs all 1.4.4-4 [12.5 kB]
Get:144 http://172.17.4.1/private trixie-staging/main armhf python3-attr all 23.1.0-2 [67.1 kB]
Get:145 http://172.17.4.1/private trixie-staging/main armhf python3-tz all 2023.3.post1-1 [30.8 kB]
Get:146 http://172.17.4.1/private trixie-staging/main armhf python3-babel all 2.10.3-2 [99.9 kB]
Get:147 http://172.17.4.1/private trixie-staging/main armhf python3-brotli armhf 1.0.9-2+b3 [278 kB]
Get:148 http://172.17.4.1/private trixie-staging/main armhf python3-certifi all 2023.7.22-1 [150 kB]
Get:149 http://172.17.4.1/private trixie-staging/main armhf python3-chardet all 5.2.0+dfsg-1 [107 kB]
Get:150 http://172.17.4.1/private trixie-staging/main armhf python3-charset-normalizer all 3.3.0-1 [51.0 kB]
Get:151 http://172.17.4.1/private trixie-staging/main armhf python3-numpy armhf 1:1.24.2-1 [3826 kB]
Get:152 http://172.17.4.1/private trixie-staging/main armhf python3-contourpy armhf 1.0.7-1 [141 kB]
Get:153 http://172.17.4.1/private trixie-staging/main armhf python3-cycler all 0.11.0-1 [8020 B]
Get:154 http://172.17.4.1/private trixie-staging/main armhf python3-six all 1.16.0-4 [17.5 kB]
Get:155 http://172.17.4.1/private trixie-staging/main armhf python3-dateutil all 2.8.2-3 [78.4 kB]
Get:156 http://172.17.4.1/private trixie-staging/main armhf python3-decorator all 5.1.1-5 [15.1 kB]
Get:157 http://172.17.4.1/private trixie-staging/main armhf python3-roman all 3.3-3 [9880 B]
Get:158 http://172.17.4.1/private trixie-staging/main armhf python3-docutils all 0.19+dfsg-8 [382 kB]
Get:159 http://172.17.4.1/private trixie-staging/main armhf python3-scipy armhf 1.10.1-2+rpi1 [13.6 MB]
Get:160 http://172.17.4.1/private trixie-staging/main armhf python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB]
Get:161 http://172.17.4.1/private trixie-staging/main armhf python3-mpmath all 1.2.1-2 [418 kB]
Get:162 http://172.17.4.1/private trixie-staging/main armhf python3-sympy all 1.12-6 [3868 kB]
Get:163 http://172.17.4.1/private trixie-staging/main armhf python3-fs all 2.4.16-2 [95.2 kB]
Get:164 http://172.17.4.1/private trixie-staging/main armhf python3-lxml armhf 4.9.3-1 [1039 kB]
Get:165 http://172.17.4.1/private trixie-staging/main armhf python3-lz4 armhf 4.0.2+dfsg-1+b1 [23.9 kB]
Get:166 http://172.17.4.1/private trixie-staging/main armhf unicode-data all 15.1.0-1 [8547 kB]
Get:167 http://172.17.4.1/private trixie-staging/main armhf python3-fonttools armhf 4.38.0-1 [1047 kB]
Get:168 http://172.17.4.1/private trixie-staging/main armhf python3-idna all 3.3-2 [39.1 kB]
Get:169 http://172.17.4.1/private trixie-staging/main armhf python3-imagesize all 1.4.1-1 [6688 B]
Get:170 http://172.17.4.1/private trixie-staging/main armhf python3-iniconfig all 1.1.1-2 [6396 B]
Get:171 http://172.17.4.1/private trixie-staging/main armhf python3-markupsafe armhf 2.1.3-1 [12.8 kB]
Get:172 http://172.17.4.1/private trixie-staging/main armhf python3-jinja2 all 3.1.2-1 [119 kB]
Get:173 http://172.17.4.1/private trixie-staging/main armhf python3-kiwisolver armhf 1.4.4-1 [52.3 kB]
Get:174 http://172.17.4.1/private trixie-staging/main armhf python3-pil armhf 10.0.0-1 [437 kB]
Get:175 http://172.17.4.1/private trixie-staging/main armhf python3-tk armhf 3.11.5-1 [95.9 kB]
Get:176 http://172.17.4.1/private trixie-staging/main armhf python3-pil.imagetk armhf 10.0.0-1 [75.2 kB]
Get:177 http://172.17.4.1/private trixie-staging/main armhf python3-pyparsing all 3.1.1-1 [145 kB]
Get:178 http://172.17.4.1/private trixie-staging/main armhf python3-packaging all 23.1-1 [37.4 kB]
Get:179 http://172.17.4.1/private trixie-staging/main armhf python3-matplotlib armhf 3.6.3-1 [7453 kB]
Get:180 http://172.17.4.1/private trixie-staging/main armhf sphinx-common all 5.3.0-7 [652 kB]
Get:181 http://172.17.4.1/private trixie-staging/main armhf python3-pygments all 2.15.1+dfsg-1 [817 kB]
Get:182 http://172.17.4.1/private trixie-staging/main armhf python3-urllib3 all 1.26.18-1 [116 kB]
Get:183 http://172.17.4.1/private trixie-staging/main armhf python3-requests all 2.31.0+dfsg-1 [68.6 kB]
Get:184 http://172.17.4.1/private trixie-staging/main armhf python3-snowballstemmer all 2.2.0-4 [58.0 kB]
Get:185 http://172.17.4.1/private trixie-staging/main armhf python3-sphinx all 5.3.0-7 [550 kB]
Get:186 http://172.17.4.1/private trixie-staging/main armhf python3-numpydoc all 1.5.0-1 [43.0 kB]
Get:187 http://172.17.4.1/private trixie-staging/main armhf python3-pandas-lib armhf 1.5.3+dfsg-6 [3000 kB]
Get:188 http://172.17.4.1/private trixie-staging/main armhf python3-pandas all 1.5.3+dfsg-6 [2886 kB]
Get:189 http://172.17.4.1/private trixie-staging/main armhf python3-pluggy all 1.3.0-1 [25.1 kB]
Get:190 http://172.17.4.1/private trixie-staging/main armhf python3-psutil armhf 5.9.5-1 [190 kB]
Get:191 http://172.17.4.1/private trixie-staging/main armhf python3-pysam armhf 0.20.0+ds-3+rpi1 [2017 kB]
Get:192 http://172.17.4.1/private trixie-staging/main armhf python3-pytest all 7.4.3-1 [239 kB]
Get:193 http://172.17.4.1/private trixie-staging/main armhf python3-yaml armhf 6.0.1-1 [108 kB]
Get:194 http://172.17.4.1/private trixie-staging/main armhf zip armhf 3.0-13 [207 kB]
Get:195 http://172.17.4.1/private trixie-staging/main armhf unzip armhf 6.0-28 [147 kB]
Get:196 http://172.17.4.1/private trixie-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:197 http://172.17.4.1/private trixie-staging/main armhf r-base-core armhf 4.3.2-1 [26.4 MB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libhtscodecs2:armhf (1.5.2-1) ...
Setting up media-types (10.1.0) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libgraphite2-3:armhf (1.3.14-1) ...
Setting up liblcms2-2:armhf (2.14-2) ...
Setting up libpixman-1-0:armhf (0.42.2-1) ...
Setting up libsharpyuv0:armhf (1.3.2-0.3) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up liblerc4:armhf (4.0.0+ds-3) ...
Setting up bsdextrautils (2.39.2-5) ...
Setting up libdatrie1:armhf (0.2.13-2+b2) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:armhf (0.2.5-1) ...
Setting up libglib2.0-0:armhf (2.78.0-2+rpi1) ...
No schema files found: doing nothing.
Setting up fonts-lyx (2.3.7-1) ...
Setting up unzip (6.0-28) ...
Setting up libpython3.11-stdlib:armhf (3.11.6-3) ...
Setting up libdebhelper-perl (13.11.7) ...
Setting up libbrotli1:armhf (1.0.9-2+b3) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up libnghttp2-14:armhf (1.57.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-13) ...
Setting up m4 (1.4.19-4) ...
Setting up libqhull-r8.0:armhf (2020.2-6) ...
Setting up file (1:5.45-2) ...
Setting up libjbig0:armhf (2.1-6.1) ...
Setting up python-babel-localedata (2.10.3-2) ...
Setting up unicode-data (15.1.0-1) ...
Setting up zip (3.0-13) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libexpat1-dev:armhf (2.5.0-2) ...
Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ...
Setting up libx11-data (2:1.8.7-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libfribidi0:armhf (1.0.13-3) ...
Setting up libimagequant0:armhf (2.17.0-1) ...
Setting up fonts-dejavu-mono (2.37-8) ...
Setting up libpng16-16:armhf (1.6.40-2) ...
Setting up libtcl8.6:armhf (8.6.13+dfsg-2) ...
Setting up autopoint (0.21-13) ...
Setting up fonts-dejavu-core (2.37-8) ...
Setting up libdpkg-perl (1.22.1+rpi1) ...
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Setting up autoconf (2.71-3) ...
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Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Setting up mount (2.39.2-5) ...
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Setting up libtiff6:armhf (4.5.1+git230720-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libjson-perl (4.10000-1) ...
Setting up libopenjp2-7:armhf (2.5.0-2) ...
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Setting up libthai-data (0.1.29-1) ...
Setting up libssh2-1:armhf (1.11.0-2) ...
Setting up sgml-base (1.31) ...
Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
Setting up python-matplotlib-data (3.6.3-1) ...
Setting up openssl (3.0.11-1) ...
Setting up libwebpmux3:armhf (1.3.2-0.3) ...
Setting up libbsd0:armhf (0.11.7-4) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up xdg-utils (1.1.3-4.1) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up bedtools (2.31.0+dfsg-1) ...
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up python3.11 (3.11.6-3) ...
Setting up libice6:armhf (2:1.0.10-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.11.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.15-1) ...
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Setting up libxcb-render0:armhf (1.15-1) ...
Setting up fontconfig-config (2.14.2-6) ...
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Setting up libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Setting up python3 (3.11.4-5) ...
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Setting up python3-markupsafe (2.1.3-1) ...
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Setting up python3-tz (2023.3.post1-1) ...
Setting up dpkg-dev (1.22.1+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up python3-six (1.16.0-4) ...
Setting up dh-autoreconf (20) ...
Setting up libthai0:armhf (0.1.29-1) ...
Setting up ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
140 added, 0 removed; done.
Setting up python3-roman (3.3-3) ...
Setting up python3-decorator (5.1.1-5) ...
Setting up python3-jinja2 (3.1.2-1) ...
Setting up python3-packaging (23.1-1) ...
Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
Setting up python3-pyparsing (3.1.1-1) ...
Setting up libfreetype6:armhf (2.13.2+dfsg-1) ...
Setting up python3-certifi (2023.7.22-1) ...
Setting up python3-snowballstemmer (2.2.0-4) ...
Setting up libpython3.11-dev:armhf (3.11.6-3) ...
Setting up python3-brotli (1.0.9-2+b3) ...
Setting up python3-cycler (0.11.0-1) ...
Setting up python3-kiwisolver (1.4.4-1) ...
Setting up python3-idna (3.3-2) ...
Setting up cython3 (0.29.36-1) ...
Setting up ucf (3.0043+nmu1) ...
Setting up libjs-sphinxdoc (5.3.0-7) ...
Setting up python3-urllib3 (1.26.18-1) ...
Setting up python3-pluggy (1.3.0-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up xml-core (0.18+nmu1) ...
Setting up libxslt1.1:armhf (1.1.35-1) ...
Setting up libcurl4:armhf (8.4.0-2+rpi1) ...
Setting up libx11-6:armhf (2:1.8.7-1) ...
Setting up libharfbuzz0b:armhf (8.0.1-1) ...
Setting up python3-dateutil (2.8.2-3) ...
Setting up libfontconfig1:armhf (2.14.2-6) ...
Setting up python3-mpmath (1.2.1-2) ...
Setting up python3-lib2to3 (3.11.5-1) ...
Setting up python3-appdirs (1.4.4-4) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up liblbfgsb0:armhf (3.0+dfsg.4-1) ...
Setting up python3-imagesize (1.4.1-1) ...
Setting up python3-pkg-resources (68.1.2-2) ...
Setting up python3-distutils (3.11.5-1) ...
Setting up python3-iniconfig (1.1.1-2) ...
Setting up python3-sympy (1.12-6) ...
Setting up python3-attr (23.1.0-2) ...
Setting up libpaper1:armhf (1.1.29) ...
Creating config file /etc/papersize with new version
Setting up fontconfig (2.14.2-6) ...
Regenerating fonts cache... done.
Setting up libhts3:armhf (1.17+ds-1) ...
Setting up python3-pysam (0.20.0+ds-3+rpi1) ...
Setting up libpython3-dev:armhf (3.11.4-5) ...
Setting up python3-setuptools (68.1.2-2) ...
Setting up libxrender1:armhf (1:0.9.10-1.1) ...
Setting up python3-babel (2.10.3-2) ...
update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode
Setting up python3-lz4 (4.0.2+dfsg-1+b1) ...
Setting up python3.11-dev (3.11.6-3) ...
Setting up python3-charset-normalizer (3.3.0-1) ...
Setting up python3-pytest (7.4.3-1) ...
Setting up python3-alabaster (0.7.12-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpango-1.0-0:armhf (1.51.0+ds-2) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up python3-all (3.11.4-5) ...
Setting up python3-yaml (6.0.1-1) ...
Setting up libpaper-utils (1.1.29) ...
Setting up man-db (2.11.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:armhf (1.18.0-1) ...
Setting up python3-fs (2.4.16-2) ...
Setting up python3-pygments (2.15.1+dfsg-1) ...
Setting up python3-chardet (5.2.0+dfsg-1) ...
Setting up libpython3-all-dev:armhf (3.11.4-5) ...
Setting up libraqm0:armhf (0.10.1-1) ...
Setting up sphinx-common (5.3.0-7) ...
Setting up python3-dev (3.11.4-5) ...
Setting up python3-requests (2.31.0+dfsg-1) ...
Setting up libxt6:armhf (1:1.2.1-1.1) ...
Setting up python3-numpy (1:1.24.2-1) ...
Setting up python3-lxml:armhf (4.9.3-1) ...
Setting up python3-contourpy (1.0.7-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.51.0+ds-2) ...
Setting up libpangocairo-1.0-0:armhf (1.51.0+ds-2) ...
Setting up dh-python (6.20231025) ...
Setting up python3-all-dev (3.11.4-5) ...
Setting up libxft2:armhf (2.3.6-1) ...
Setting up python3-scipy (1.10.1-2+rpi1) ...
Setting up libtk8.6:armhf (8.6.13-2) ...
Setting up python3-pandas-lib:armhf (1.5.3+dfsg-6) ...
Setting up debhelper (13.11.7) ...
Setting up python3-pandas (1.5.3+dfsg-6) ...
Setting up r-base-core (4.3.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ...
Setting up blt (2.5.3+dfsg-4.1) ...
Setting up python3-tk:armhf (3.11.5-1) ...
Setting up python3-pil:armhf (10.0.0-1) ...
Setting up python3-pil.imagetk:armhf (10.0.0-1) ...
Setting up python3-ufolib2 (0.16.0+dfsg1-1) ...
Setting up python3-fonttools (4.38.0-1) ...
Setting up python3-matplotlib (3.6.3-1) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
Processing triggers for sgml-base (1.31) ...
Setting up docutils-common (0.19+dfsg-8) ...
Processing triggers for sgml-base (1.31) ...
Setting up python3-docutils (0.19+dfsg-8) ...
Setting up python3-sphinx (5.3.0-7) ...
Setting up python3-numpydoc (1.5.0-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 bedtools_2.31.0+dfsg-1 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 blt_2.5.3+dfsg-4.1 bsdextrautils_2.39.2-5 bsdutils_1:2.39.2-5 build-essential_12.9 bzip2_1.0.8-5+b2 ca-certificates_20230311 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 cython3_0.29.36-1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.7 debianutils_5.14 dh-autoreconf_20 dh-python_6.20231025 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 docutils-common_0.19+dfsg-8 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 fontconfig_2.14.2-6 fontconfig-config_2.14.2-6 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lyx_2.3.7-1 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 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man-db_2.11.2-3 mawk_1.3.4.20230808-1 media-types_10.1.0 mount_2.39.2-5 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 openssl_3.0.11-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 python-babel-localedata_2.10.3-2 python-matplotlib-data_3.6.3-1 python3_3.11.4-5 python3-alabaster_0.7.12-1 python3-all_3.11.4-5 python3-all-dev_3.11.4-5 python3-appdirs_1.4.4-4 python3-attr_23.1.0-2 python3-babel_2.10.3-2 python3-brotli_1.0.9-2+b3 python3-certifi_2023.7.22-1 python3-chardet_5.2.0+dfsg-1 python3-charset-normalizer_3.3.0-1 python3-contourpy_1.0.7-1 python3-cycler_0.11.0-1 python3-dateutil_2.8.2-3 python3-decorator_5.1.1-5 python3-dev_3.11.4-5 python3-distutils_3.11.5-1 python3-docutils_0.19+dfsg-8 python3-fonttools_4.38.0-1 python3-fs_2.4.16-2 python3-idna_3.3-2 python3-imagesize_1.4.1-1 python3-iniconfig_1.1.1-2 python3-jinja2_3.1.2-1 python3-kiwisolver_1.4.4-1 python3-lib2to3_3.11.5-1 python3-lxml_4.9.3-1 python3-lz4_4.0.2+dfsg-1+b1 python3-markupsafe_2.1.3-1 python3-matplotlib_3.6.3-1 python3-minimal_3.11.4-5 python3-mpmath_1.2.1-2 python3-numpy_1:1.24.2-1 python3-numpydoc_1.5.0-1 python3-packaging_23.1-1 python3-pandas_1.5.3+dfsg-6 python3-pandas-lib_1.5.3+dfsg-6 python3-pil_10.0.0-1 python3-pil.imagetk_10.0.0-1 python3-pkg-resources_68.1.2-2 python3-pluggy_1.3.0-1 python3-psutil_5.9.5-1 python3-pygments_2.15.1+dfsg-1 python3-pyparsing_3.1.1-1 python3-pysam_0.20.0+ds-3+rpi1 python3-pytest_7.4.3-1 python3-requests_2.31.0+dfsg-1 python3-roman_3.3-3 python3-scipy_1.10.1-2+rpi1 python3-setuptools_68.1.2-2 python3-six_1.16.0-4 python3-snowballstemmer_2.2.0-4 python3-sphinx_5.3.0-7 python3-sympy_1.12-6 python3-tk_3.11.5-1 python3-tz_2023.3.post1-1 python3-ufolib2_0.16.0+dfsg1-1 python3-urllib3_1.26.18-1 python3-yaml_6.0.1-1 python3.11_3.11.6-3 python3.11-dev_3.11.6-3 python3.11-minimal_3.11.6-3 r-base-core_4.3.2-1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sphinx-common_5.3.0-7 sysvinit-utils_3.08-3 tar_1.34+dfsg-1.2 tk8.6-blt2.5_2.5.3+dfsg-4.1 tzdata_2023c-10 ucf_3.0043+nmu1 unicode-data_15.1.0-1 unzip_6.0-28 usr-is-merged_37 util-linux_2.39.2-5 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xml-core_0.18+nmu1 xz-utils_5.4.4-0.1 zip_3.0-13 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: python-pybedtools
Binary: pybedtools-bin, python3-pybedtools, python-pybedtools-doc
Architecture: any all
Version: 0.9.1-1
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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Checksums-Sha256:
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Files:
bbaaa1a701513241e8acb0fdb918d9c1 12032824 python-pybedtools_0.9.1.orig.tar.xz
e24bc8fbd3871f4b389b0a354cc76adf 29948 python-pybedtools_0.9.1-1.debian.tar.xz
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gpgv: Signature made Wed Nov 1 06:51:36 2023 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.9.1-1.dsc: no acceptable signature found
dpkg-source: info: extracting python-pybedtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking python-pybedtools_0.9.1.orig.tar.xz
dpkg-source: info: unpacking python-pybedtools_0.9.1-1.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
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-8c77828a-7aad-4906-b553-5ae8da9f5c49
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package python-pybedtools
dpkg-buildpackage: info: source version 0.9.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from python-pybedtools-0.9.1/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:310: python3.11 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:265: 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:265: UserWarning: Unknown distribution option: 'language_level'
warnings.warn(msg)
running cythonize
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<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:310: /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:265: UserWarning: Unknown distribution option: 'language_level'
warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/bedtool.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/filenames.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/genome_registry.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/helpers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/logger.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/parallel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/paths.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/settings.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/regression_tests.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_1.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_contrib.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_helpers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_issues.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_len_leak.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_pathlib.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/tfuncs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_iter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
running egg_info
creating pybedtools.egg-info
writing pybedtools.egg-info/PKG-INFO
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pybedtools'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _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_3.11_pybedtools/build/pybedtools
copying pybedtools/cbedtools.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/cbedtools.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/cbedtools.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/featurefuncs.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
copying pybedtools/featurefuncs.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/bedFile.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/bedFile.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/fileType.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/fileType.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/gzstream.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/gzstream.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
copying pybedtools/test/data/1000genomes-example.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/b.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/c.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/d.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/small.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/x.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/x.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/data/y.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/mpl-expected.png -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_cases.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
creating build
creating build/temp.linux-armv7l-cpython-311
creating build/temp.linux-armv7l-cpython-311/pybedtools
creating build/temp.linux-armv7l-cpython-311/pybedtools/include
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/cbedtools.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/cbedtools.o
In file included from pybedtools/cbedtools.cpp:802:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pybedtools/cbedtools.o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so
building 'pybedtools.featurefuncs' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/featurefuncs.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/featurefuncs.o
In file included from pybedtools/featurefuncs.cpp:802:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pybedtools/featurefuncs.o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.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:265: UserWarning: Unknown distribution option: 'language_level'
warnings.warn(msg)
running develop
/usr/lib/python3/dist-packages/setuptools/command/develop.py:40: 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
creating build/temp.linux-aarch64-cpython-311
creating build/temp.linux-aarch64-cpython-311/pybedtools
creating build/temp.linux-aarch64-cpython-311/pybedtools/include
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/cbedtools.cpp -o build/temp.linux-aarch64-cpython-311/pybedtools/cbedtools.o
In file included from pybedtools/cbedtools.cpp:802:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-311/pybedtools/include/bedFile.o
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-311/pybedtools/include/fileType.o
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-311/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/pybedtools/cbedtools.o build/temp.linux-aarch64-cpython-311/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-311/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o /<<PKGBUILDDIR>>/pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so
building 'pybedtools.featurefuncs' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/featurefuncs.cpp -o build/temp.linux-aarch64-cpython-311/pybedtools/featurefuncs.o
In file included from pybedtools/featurefuncs.cpp:802:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/bedFile.cpp -o build/temp.linux-aarch64-cpython-311/pybedtools/include/bedFile.o
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/fileType.cpp -o build/temp.linux-aarch64-cpython-311/pybedtools/include/fileType.o
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/gzstream.cpp -o build/temp.linux-aarch64-cpython-311/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-aarch64-cpython-311/pybedtools/featurefuncs.o build/temp.linux-aarch64-cpython-311/pybedtools/include/bedFile.o build/temp.linux-aarch64-cpython-311/pybedtools/include/fileType.o build/temp.linux-aarch64-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o /<<PKGBUILDDIR>>/pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.so
Creating /<<PKGBUILDDIR>>/fakehome/.local/lib/python3.11/site-packages/pybedtools.egg-link (link to .)
Adding pybedtools 0.9.1 to easy-install.pth file
Installed /<<PKGBUILDDIR>>
Processing dependencies for pybedtools==0.9.1
Searching for six==1.16.0
Best match: six 1.16.0
Adding six 1.16.0 to easy-install.pth file
Using /usr/lib/python3/dist-packages
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Best match: pysam 0.20.0
Adding pysam 0.20.0 to easy-install.pth file
Using /usr/lib/python3/dist-packages
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Best match: numpy 1.24.2
Adding numpy 1.24.2 to easy-install.pth file
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Installing f2py3 script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Installing f2py3.11 script to /<<PKGBUILDDIR>>/fakehome/.local/bin
Using /usr/lib/python3/dist-packages
Finished processing dependencies for pybedtools==0.9.1
sphinx-build -N -b html docs/source docs/html
Running Sphinx v5.3.0
making output directory... done
[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst
[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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build succeeded, 9 warnings.
The HTML pages are in docs/html.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a -O--buildsystem=pybuild
I: pybuild pybuild:314: cp /<<PKGBUILDDIR>>/debian/mpl-expected.png /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_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
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/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:265: 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()
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copying pybedtools/test/test_len_leak.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test
creating build/lib.linux-armv7l-cpython-311/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-armv7l-cpython-311/pybedtools/contrib
creating build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pybedtools.include' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pybedtools.include' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pybedtools.include' to be distributed and are
already explicitly excluding 'pybedtools.include' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
copying pybedtools/_Window.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools
copying pybedtools/cbedtools.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-armv7l-cpython-311/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools
copying pybedtools/featurefuncs.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools
copying pybedtools/featurefuncs.pyx -> build/lib.linux-armv7l-cpython-311/pybedtools
creating build/lib.linux-armv7l-cpython-311/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include
copying pybedtools/include/bedFile.h -> build/lib.linux-armv7l-cpython-311/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include
copying pybedtools/include/fileType.h -> build/lib.linux-armv7l-cpython-311/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-armv7l-cpython-311/pybedtools/include
copying pybedtools/include/gzstream.h -> build/lib.linux-armv7l-cpython-311/pybedtools/include
copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-armv7l-cpython-311/pybedtools/include
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/test.fa -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/x.bed -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-armv7l-cpython-311/pybedtools/test/data
copying pybedtools/test/gchart-expected.png -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/mpl-expected.png -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/test_cases.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/test_merge215.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/test_merge227.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test
copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-armv7l-cpython-311/pybedtools/test
running build_ext
building 'pybedtools.cbedtools' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/cbedtools.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/cbedtools.o
In file included from pybedtools/cbedtools.cpp:802:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pybedtools/cbedtools.o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so
building 'pybedtools.featurefuncs' extension
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/featurefuncs.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/featurefuncs.o
In file included from pybedtools/featurefuncs.cpp:802:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/bedFile.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o
In file included from pybedtools/include/bedFile.cpp:12:
pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
92 | for (register short i = 0; i < _binLevels; ++i) {
| ^
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/fileType.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o
arm-linux-gnueabihf-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.11 -c pybedtools/include/gzstream.cpp -o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o
arm-linux-gnueabihf-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -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 -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-armv7l-cpython-311/pybedtools/featurefuncs.o build/temp.linux-armv7l-cpython-311/pybedtools/include/bedFile.o build/temp.linux-armv7l-cpython-311/pybedtools/include/fileType.o build/temp.linux-armv7l-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/arm-linux-gnueabihf -lstdc++ -lz -o build/lib.linux-armv7l-cpython-311/pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.so
creating build/bdist.linux-armv7l
creating build/bdist.linux-armv7l/egg
creating build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/__init__.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/bedtool.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/filenames.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/genome_registry.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/helpers.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/logger.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/parallel.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/paths.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/settings.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/stats.py -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/version.py -> build/bdist.linux-armv7l/egg/pybedtools
creating build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/__init__.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/genomepy_integration.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/regression_tests.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_1.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_cbedtools.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_contrib.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_gzip_support.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_helpers.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_issues.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_len_leak.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_pathlib.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/tfuncs.py -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_iter.py -> build/bdist.linux-armv7l/egg/pybedtools/test
creating build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/__init__.py -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/164.gtf -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/a.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/a.igv_script -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/a.links.html -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/b.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/bedpe.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/c.gff -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/d.gff -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/exons.gff -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/expand_test.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.cram -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.gff -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/genome.fa -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/hg19.gff -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/issue319.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/issue_121.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/m1.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/reads.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/small.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/small.fastq -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test.fa -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test.fa.fai -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/v.vcf -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/venn.b.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/venn.c.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/x.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/x.bed -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/data/y.bam -> build/bdist.linux-armv7l/egg/pybedtools/test/data
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/gchart-expected.png -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/mpl-expected.png -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_cases.yaml -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_merge215.yaml -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_merge227.yaml -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-armv7l/egg/pybedtools/test
copying build/lib.linux-armv7l-cpython-311/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-armv7l/egg/pybedtools/test
creating build/bdist.linux-armv7l/egg/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/__init__.py -> build/bdist.linux-armv7l/egg/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/bigbed.py -> build/bdist.linux-armv7l/egg/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-armv7l/egg/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-armv7l/egg/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/venn_maker.py -> build/bdist.linux-armv7l/egg/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/bigwig.py -> build/bdist.linux-armv7l/egg/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-311/pybedtools/contrib/plotting.py -> build/bdist.linux-armv7l/egg/pybedtools/contrib
copying build/lib.linux-armv7l-cpython-311/pybedtools/_Window.pyx -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.cpp -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.pxd -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.pyx -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/featurefuncs.cpp -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/featurefuncs.pyx -> build/bdist.linux-armv7l/egg/pybedtools
creating build/bdist.linux-armv7l/egg/pybedtools/include
copying build/lib.linux-armv7l-cpython-311/pybedtools/include/bedFile.cpp -> build/bdist.linux-armv7l/egg/pybedtools/include
copying build/lib.linux-armv7l-cpython-311/pybedtools/include/bedFile.h -> build/bdist.linux-armv7l/egg/pybedtools/include
copying build/lib.linux-armv7l-cpython-311/pybedtools/include/fileType.cpp -> build/bdist.linux-armv7l/egg/pybedtools/include
copying build/lib.linux-armv7l-cpython-311/pybedtools/include/fileType.h -> build/bdist.linux-armv7l/egg/pybedtools/include
copying build/lib.linux-armv7l-cpython-311/pybedtools/include/gzstream.cpp -> build/bdist.linux-armv7l/egg/pybedtools/include
copying build/lib.linux-armv7l-cpython-311/pybedtools/include/gzstream.h -> build/bdist.linux-armv7l/egg/pybedtools/include
copying build/lib.linux-armv7l-cpython-311/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-armv7l/egg/pybedtools/include
copying build/lib.linux-armv7l-cpython-311/pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/egg/pybedtools
copying build/lib.linux-armv7l-cpython-311/pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/egg/pybedtools
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/bedtool.py to bedtool.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/filenames.py to filenames.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/genome_registry.py to genome_registry.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/helpers.py to helpers.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/logger.py to logger.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/parallel.py to parallel.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/paths.py to paths.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/settings.py to settings.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/stats.py to stats.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/version.py to version.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/genomepy_integration.py to genomepy_integration.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/regression_tests.py to regression_tests.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_1.py to test_1.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_cbedtools.py to test_cbedtools.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_contrib.py to test_contrib.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_gzip_support.py to test_gzip_support.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_helpers.py to test_helpers.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_issues.py to test_issues.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_len_leak.py to test_len_leak.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_pathlib.py to test_pathlib.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/tfuncs.py to tfuncs.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/test_iter.py to test_iter.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/test/data/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/contrib/__init__.py to __init__.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/contrib/bigbed.py to bigbed.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/contrib/intersection_matrix.py to intersection_matrix.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/contrib/long_range_interaction.py to long_range_interaction.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/contrib/venn_maker.py to venn_maker.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/contrib/bigwig.py to bigwig.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/contrib/plotting.py to plotting.cpython-311.pyc
creating stub loader for pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so
creating stub loader for pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.so
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/cbedtools.py to cbedtools.cpython-311.pyc
byte-compiling build/bdist.linux-armv7l/egg/pybedtools/featurefuncs.py to featurefuncs.cpython-311.pyc
creating build/bdist.linux-armv7l/egg/EGG-INFO
copying pybedtools.egg-info/PKG-INFO -> build/bdist.linux-armv7l/egg/EGG-INFO
copying pybedtools.egg-info/SOURCES.txt -> build/bdist.linux-armv7l/egg/EGG-INFO
copying pybedtools.egg-info/dependency_links.txt -> build/bdist.linux-armv7l/egg/EGG-INFO
copying pybedtools.egg-info/not-zip-safe -> build/bdist.linux-armv7l/egg/EGG-INFO
copying pybedtools.egg-info/requires.txt -> build/bdist.linux-armv7l/egg/EGG-INFO
copying pybedtools.egg-info/top_level.txt -> build/bdist.linux-armv7l/egg/EGG-INFO
writing build/bdist.linux-armv7l/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/pybedtools-0.9.1-py3.11-linux-armv7l.egg' and adding 'build/bdist.linux-armv7l/egg' to it
removing 'build/bdist.linux-armv7l/egg' (and everything under it)
Processing pybedtools-0.9.1-py3.11-linux-armv7l.egg
creating /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/lib/python3.11/site-packages/pybedtools-0.9.1-py3.11-linux-armv7l.egg
Extracting pybedtools-0.9.1-py3.11-linux-armv7l.egg to /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/lib/python3.11/site-packages
Adding pybedtools 0.9.1 to easy-install.pth file
Installed /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/lib/python3.11/site-packages/pybedtools-0.9.1-py3.11-linux-armv7l.egg
Processing dependencies for pybedtools==0.9.1
Searching for six==1.16.0
Best match: six 1.16.0
Adding six 1.16.0 to easy-install.pth file
detected new path './pybedtools-0.9.1-py3.11-linux-armv7l.egg'
Using /usr/lib/python3/dist-packages
Searching for pysam==0.20.0
Best match: pysam 0.20.0
Adding pysam 0.20.0 to easy-install.pth file
Using /usr/lib/python3/dist-packages
Searching for numpy==1.24.2
Best match: numpy 1.24.2
Adding numpy 1.24.2 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 f2py3.11 script to /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/.local/bin
Using /usr/lib/python3/dist-packages
Finished processing dependencies for pybedtools==0.9.1
I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build; python3.11 -m pytest -k "not test_chromsizes"
============================= test session starts ==============================
platform linux -- Python 3.11.6, pytest-7.4.3, pluggy-1.3.0
rootdir: /<<PKGBUILDDIR>>
collected 510 items / 2 deselected / 508 selected
pybedtools/test/test_1.py .............................................. [ 9%]
.......................x..x.x...... [ 15%]
pybedtools/test/test_cbedtools.py ...................................... [ 23%]
. [ 23%]
pybedtools/test/test_contrib.py .. [ 24%]
pybedtools/test/test_gzip_support.py ........ [ 25%]
pybedtools/test/test_helpers.py ...... [ 26%]
pybedtools/test/test_issues.py ......................................... [ 34%]
. [ 35%]
pybedtools/test/test_iter.py ........................................... [ 43%]
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pybedtools/test/test_pathlib.py ... [100%]
================ 505 passed, 2 deselected, 3 xfailed in 20.36s =================
I: pybuild pybuild:340: 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 v5.3.0
making output directory... done
[autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst
[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
building [mo]: targets for 0 po files that are out of date
building [doctest]: targets for 48 source files that are out of date
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/usr/lib/python3/dist-packages/numpydoc/docscrape.py:460: UserWarning: Unknown section Example in the docstring of tag_bedpe in /<<PKGBUILDDIR>>/pybedtools/contrib/long_range_interaction.py.
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/<<PKGBUILDDIR>>/docs/source/autodocs/pybedtools.contrib.plotting.Track.rst:155: WARNING: autosummary: failed to import Track.colorbar.
Possible hints:
* AttributeError: type object 'Track' has no attribute 'Track'
* KeyError: 'Track'
* ImportError:
* AttributeError: type object 'Track' has no attribute 'colorbar'
* ModuleNotFoundError: No module named 'pybedtools.contrib.plotting.Track'; 'pybedtools.contrib.plotting' is not a package
* ModuleNotFoundError: No module named 'Track'
/<<PKGBUILDDIR>>/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy<https://github.com/vanheeringen-lab/genomepy/>".
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
running tests...
Document: filtering
-------------------
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---------------------------
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----------------------------------
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Document: topical-bam
---------------------
[E::idx_find_and_load] Could not retrieve index file for '/<<PKGBUILDDIR>>/pybedtools/test/data/x.bam'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/pybedtools.5vuco975.tmp'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/pybedtools.5vuco975.tmp'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/pybedtools.5vuco975.tmp'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/pybedtools.5vuco975.tmp'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/pybedtools.5vuco975.tmp'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/pybedtools.5vuco975.tmp'
[E::idx_find_and_load] Could not retrieve index file for '/tmp/pybedtools.5vuco975.tmp'
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-------------------------------
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------------------------
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-----------------
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10 tests in 1 items.
10 passed and 0 failed.
Test passed.
Doctest summary
===============
224 tests
0 failures in tests
0 failures in setup code
0 failures in cleanup code
build succeeded, 2 warnings.
Testing of doctests in the sources finished, look at the results in build/doctest/output.txt.
Testing of doctests in the sources finished, look at the results in build/doctest/output.txt.
make[1]: Leaving directory '/<<PKGBUILDDIR>>/docs'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=pybuild
dh_prep -a -O--buildsystem=pybuild
dh_auto_install -a -O--buildsystem=pybuild
I: pybuild base:310: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/python3-pybedtools
/<<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:265: 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()
running build
running build_py
copying pybedtools/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
running egg_info
writing pybedtools.egg-info/PKG-INFO
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.c' under directory 'pybedtools'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:204: _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)
running build_ext
running install_lib
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__init__.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/bedtool.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/filenames.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/genome_registry.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/helpers.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/logger.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/parallel.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/paths.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/settings.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/stats.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__init__.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/genomepy_integration.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/regression_tests.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_1.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_cbedtools.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_contrib.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_gzip_support.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_helpers.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_issues.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_len_leak.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_pathlib.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/tfuncs.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_iter.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/__init__.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/1000genomes-example.vcf -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/164.gtf -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/a.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/a.igv_script -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/a.links.html -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/b.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/bedpe.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/bedpe2.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/c.gff -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/d.gff -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/democonfig.yaml -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/example.narrowPeak -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/exons.gff -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/expand_test.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.1.100.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.1.100.bam.bai -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.50.200.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.50.200.bam.bai -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.cram -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.gff -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.gff.gz -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.othersort.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.sorted.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/gdc.sorted.bam.bai -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/genome.fa -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/hg19.gff -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/hg38-base.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/hg38-problem.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/issue319.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/issue319.out.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/issue319.vcf.gz -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/issue_121.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/m1.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/mm9.bed12 -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/multibamcov_test.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/reads.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/small.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/small.fastq -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/snps.bed.gz -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/tag_test1.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/tag_test2.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test.fa -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test.fa.fai -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test_bedpe.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test_peaks.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/test_tsses.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/v.vcf -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/vcf-stderr-test.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/vcf-stderr-test.vcf -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/venn.b.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/venn.c.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/x.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/x.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/y.bam -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/1000genomes-example.vcf.gz -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/a.bed.gz -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data/a.bed.gz.tbi -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/gchart-expected.png -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/mpl-expected.png -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/prevent_open_file_regression -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_cases.yaml -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_merge215.yaml -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_merge227.yaml -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_shuffle215.yaml -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/test_shuffle227.yaml -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_1.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_cbedtools.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/tfuncs.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_contrib.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_gzip_support.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_helpers.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_issues.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_iter.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_len_leak.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/__pycache__/test_pathlib.cpython-311-pytest-7.4.3.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__pycache__
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/__init__.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/bigbed.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/intersection_matrix.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/long_range_interaction.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/venn_maker.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/bigwig.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/plotting.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/__pycache__/bigwig.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/__pycache__/bigbed.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/__pycache__/venn_maker.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/__pycache__/long_range_interaction.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib/__pycache__/intersection_matrix.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/_Window.pyx -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.cpp -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.pxd -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.pyx -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.cpp -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.pyx -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/bedFile.cpp -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/bedFile.h -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/fileType.cpp -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/fileType.h -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/gzstream.cpp -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/gzstream.h -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include/lineFileUtilities.h -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/include
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.cpython-311-arm-linux-gnueabihf.so -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
creating /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/__init__.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/helpers.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/settings.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/filenames.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/genome_registry.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/logger.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/bedtool.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/stats.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/version.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/__pycache__/paths.cpython-311.pyc -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__pycache__
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/version.py -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/foo.bed -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages
copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/genome.txt -> /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/bedtool.py to bedtool.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/filenames.py to filenames.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/genome_registry.py to genome_registry.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/helpers.py to helpers.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/logger.py to logger.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/parallel.py to parallel.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/paths.py to paths.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/settings.py to settings.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/stats.py to stats.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/genomepy_integration.py to genomepy_integration.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/regression_tests.py to regression_tests.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_1.py to test_1.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_cbedtools.py to test_cbedtools.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_contrib.py to test_contrib.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_gzip_support.py to test_gzip_support.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_helpers.py to test_helpers.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_issues.py to test_issues.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_len_leak.py to test_len_leak.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_pathlib.py to test_pathlib.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/tfuncs.py to tfuncs.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/test_iter.py to test_iter.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/test/data/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/__init__.py to __init__.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/bigbed.py to bigbed.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/intersection_matrix.py to intersection_matrix.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/long_range_interaction.py to long_range_interaction.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/venn_maker.py to venn_maker.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/bigwig.py to bigwig.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/contrib/plotting.py to plotting.cpython-311.pyc
byte-compiling /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools/version.py to version.cpython-311.pyc
running install_egg_info
Copying pybedtools.egg-info to /<<PKGBUILDDIR>>/debian/python3-pybedtools/usr/lib/python3.11/dist-packages/pybedtools-0.9.1.egg-info
Skipping SOURCES.txt
running install_scripts
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
rm -f debian/python3-pybedtools/usr/lib/python3*/dist-packages/pybedtools/test/prevent_open_file_regression \
debian/python3-pybedtools/usr/lib/python3*/dist-packages/foo.bed \
debian/python3-pybedtools/usr/lib/python3*/dist-packages/genome.txt
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a -O--buildsystem=pybuild
dh_sphinxdoc -a -O--buildsystem=pybuild
dh_sphinxdoc: warning: Sphinx documentation not found
dh_installchangelogs -a -O--buildsystem=pybuild
dh_installexamples -a -O--buildsystem=pybuild
dh_python3 -a -O--buildsystem=pybuild
dh_installsystemduser -a -O--buildsystem=pybuild
dh_perl -a -O--buildsystem=pybuild
dh_link -a -O--buildsystem=pybuild
dh_strip_nondeterminism -a -O--buildsystem=pybuild
dh_compress -a -O--buildsystem=pybuild
dh_fixperms -a -O--buildsystem=pybuild
dh_missing -a -O--buildsystem=pybuild
dh_dwz -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -a -O--buildsystem=pybuild
dh_gencontrol -a -O--buildsystem=pybuild
dh_md5sums -a -O--buildsystem=pybuild
dh_builddeb -a -O--buildsystem=pybuild
dpkg-deb: building package 'python3-pybedtools-dbgsym' in '../python3-pybedtools-dbgsym_0.9.1-1_armhf.deb'.
dpkg-deb: building package 'python3-pybedtools' in '../python3-pybedtools_0.9.1-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../python-pybedtools_0.9.1-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../python-pybedtools_0.9.1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-source: info: using options from python-pybedtools-0.9.1/debian/source/options: --extend-diff-ignore=(pybedtools/version.py|docs/source/pybedtools.featurefuncs.*.rst)
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2023-11-06T05:09:55Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
python-pybedtools_0.9.1-1_armhf.changes:
----------------------------------------
Format: 1.8
Date: Fri, 27 Oct 2023 19:35:26 +0700
Source: python-pybedtools
Binary: python3-pybedtools python3-pybedtools-dbgsym
Architecture: armhf
Version: 0.9.1-1
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Lance Lin <lq27267@gmail.com>
Description:
python3-pybedtools - Python 3 wrapper around BEDTools for bioinformatics work
Closes: 1042651 1048006
Changes:
python-pybedtools (0.9.1-1) unstable; urgency=medium
.
[ Lance Lin ]
* Team upload.
* New upstream version
* d/control: Replace autopkgtest-pkg-python with autopkgtest-pkg-pybuild
* d/rules:
- Enable build tests
- Deselect test_chromsizes test, needs internet
- Build docs with sphinx-build for Sphinx 7.1 (Closes: #1042651)
- Remove autogenerated files from build
* d/python-pybedtools-doc.docs: Change sphinx docs location
* d/source/options: Ignore modified source files (Closes: #1048006)
* d/patches/yaml_safe_load.patch: Modify safe_load for full_load where needed
.
[ Andreas Tille ]
* Remove unknown files in python module directory
* Testsuite: autopkgtest-pkg-python (routine-update)
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* Remove field Testsuite on binary package python-pybedtools-doc that
duplicates source.
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Files:
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+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: python-pybedtools
Binary: python3-pybedtools python3-pybedtools-dbgsym
Architecture: armhf
Version: 0.9.1-1
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 06 Nov 2023 05:09:55 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-13),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.2),
bash (= 5.2.15-2),
bedtools (= 2.31.0+dfsg-1),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
blt (= 2.5.3+dfsg-4.1),
bsdextrautils (= 2.39.2-5),
bsdutils (= 1:2.39.2-5),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
ca-certificates (= 20230311),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-10+rpi1),
cpp-13 (= 13.2.0-5+rpi1),
cython3 (= 0.29.36-1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.7),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-python (= 6.20231025),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
docutils-common (= 0.19+dfsg-8),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
fontconfig (= 2.14.2-6),
fontconfig-config (= 2.14.2-6),
fonts-dejavu-core (= 2.37-8),
fonts-dejavu-mono (= 2.37-8),
fonts-lyx (= 2.3.7-1),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-5+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-10+rpi1),
gcc-12-base (= 12.3.0-10+rpi1),
gcc-13 (= 13.2.0-5+rpi1),
gcc-13-base (= 13.2.0-5+rpi1),
gettext (= 0.21-13),
gettext-base (= 0.21-13),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hostname (= 3.23+nmu1),
init-system-helpers (= 1.65.2),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-5+rpi1),
libatomic1 (= 13.2.0-5+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.1-1),
libaudit1 (= 1:3.1.1-1),
libbinutils (= 2.41-6+rpi1),
libblas3 (= 3.11.0-2),
libblkid1 (= 2.39.2-5),
libbrotli1 (= 1.0.9-2+b3),
libbsd0 (= 0.11.7-4),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcairo2 (= 1.18.0-1),
libcap-ng0 (= 0.8.3-1+b1),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-5+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl3-gnutls (= 8.4.0-2+rpi1),
libcurl4 (= 8.4.0-2+rpi1),
libdatrie1 (= 0.2.13-2+b2),
libdb5.3 (= 5.3.28+dfsg2-2),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.7),
libdeflate0 (= 1.18-1),
libdpkg-perl (= 1.22.1+rpi1),
libelf1 (= 0.188-2.1+rpi1),
libexpat1 (= 2.5.0-2),
libexpat1-dev (= 2.5.0-2),
libffi8 (= 3.4.4-1),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libfontconfig1 (= 2.14.2-6),
libfreetype6 (= 2.13.2+dfsg-1),
libfribidi0 (= 1.0.13-3),
libgcc-12-dev (= 12.3.0-10+rpi1),
libgcc-13-dev (= 13.2.0-5+rpi1),
libgcc-s1 (= 13.2.0-5+rpi1),
libgcrypt20 (= 1.10.2-3),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgfortran5 (= 13.2.0-5+rpi1),
libglib2.0-0 (= 2.78.0-2+rpi1),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.1-4),
libgomp1 (= 13.2.0-5+rpi1),
libgpg-error0 (= 1.47-2),
libgraphite2-3 (= 1.3.14-1),
libgssapi-krb5-2 (= 1.20.1-4),
libharfbuzz0b (= 8.0.1-1),
libhogweed6 (= 3.9.1-2),
libhts3 (= 1.17+ds-1),
libhtscodecs2 (= 1.5.2-1),
libice6 (= 2:1.0.10-1),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libimagequant0 (= 2.17.0-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libjbig0 (= 2.1-6.1),
libjpeg62-turbo (= 1:2.1.5-2),
libjs-jquery (= 3.6.1+dfsg+~3.5.14-1),
libjs-jquery-ui (= 1.13.2+dfsg-1),
libjs-sphinxdoc (= 5.3.0-7),
libjs-underscore (= 1.13.4~dfsg+~1.11.4-3),
libjson-perl (= 4.10000-1),
libk5crypto3 (= 1.20.1-4),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-4),
libkrb5support0 (= 1.20.1-4),
liblapack3 (= 3.11.0-2),
liblbfgsb0 (= 3.0+dfsg.4-1),
liblcms2-2 (= 2.14-2),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
liblerc4 (= 4.0.0+ds-3),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma5 (= 5.4.4-0.1),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libmount1 (= 2.39.2-5),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncursesw6 (= 6.4+20231016-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.57.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libopenjp2-7 (= 2.5.0-2),
libp11-kit0 (= 0.25.0-5),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpango-1.0-0 (= 1.51.0+ds-2),
libpangocairo-1.0-0 (= 1.51.0+ds-2),
libpangoft2-1.0-0 (= 1.51.0+ds-2),
libpaper-utils (= 1.1.29),
libpaper1 (= 1.1.29),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-9),
libpipeline1 (= 1.5.7-1),
libpixman-1-0 (= 0.42.2-1),
libpng16-16 (= 1.6.40-2),
libpsl5 (= 0.21.2-1+b1),
libpython3-all-dev (= 3.11.4-5),
libpython3-dev (= 3.11.4-5),
libpython3-stdlib (= 3.11.4-5),
libpython3.11 (= 3.11.6-3),
libpython3.11-dev (= 3.11.6-3),
libpython3.11-minimal (= 3.11.6-3),
libpython3.11-stdlib (= 3.11.6-3),
libqhull-r8.0 (= 2020.2-6),
libraqm0 (= 0.10.1-1),
libreadline8 (= 8.2-1.3),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg1-3),
libsasl2-modules-db (= 2.1.28+dfsg1-3),
libseccomp2 (= 2.5.4-1+rpi1+b1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libsharpyuv0 (= 1.3.2-0.3),
libsm6 (= 2:1.2.3-1),
libsmartcols1 (= 2.39.2-5),
libsqlite3-0 (= 3.43.2-1),
libssh2-1 (= 1.11.0-2),
libssl3 (= 3.0.11-1),
libstdc++-13-dev (= 13.2.0-5+rpi1),
libstdc++6 (= 13.2.0-5+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 254.5-1+rpi1),
libtasn1-6 (= 4.19.0-3),
libtcl8.6 (= 8.6.13+dfsg-2),
libthai-data (= 0.1.29-1),
libthai0 (= 0.1.29-1),
libtiff6 (= 4.5.1+git230720-1),
libtinfo6 (= 6.4+20231016-1),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtk8.6 (= 8.6.13-2),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-5+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.2-5),
libwebp7 (= 1.3.2-0.3),
libwebpdemux2 (= 1.3.2-0.3),
libwebpmux3 (= 1.3.2-0.3),
libx11-6 (= 2:1.8.7-1),
libx11-data (= 2:1.8.7-1),
libxau6 (= 1:1.0.9-1),
libxcb-render0 (= 1.15-1),
libxcb-shm0 (= 1.15-1),
libxcb1 (= 1.15-1),
libxdmcp6 (= 1:1.1.2-3),
libxext6 (= 2:1.3.4-1),
libxft2 (= 2.3.6-1),
libxml2 (= 2.9.14+dfsg-1.3),
libxrender1 (= 1:0.9.10-1.1),
libxslt1.1 (= 1.1.35-1),
libxss1 (= 1:1.2.3-1),
libxt6 (= 1:1.2.1-1.1),
libyaml-0-2 (= 0.2.5-1),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
lsb-base (= 11.6+rpi1),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.11.2-3),
mawk (= 1.3.4.20230808-1),
media-types (= 10.1.0),
ncurses-base (= 6.4+20231016-1),
ncurses-bin (= 6.4+20231016-1),
openssl (= 3.0.11-1),
patch (= 2.7.6-7),
perl (= 5.36.0-9),
perl-base (= 5.36.0-9),
perl-modules-5.36 (= 5.36.0-9),
po-debconf (= 1.0.21+nmu1),
python-babel-localedata (= 2.10.3-2),
python-matplotlib-data (= 3.6.3-1),
python3 (= 3.11.4-5),
python3-alabaster (= 0.7.12-1),
python3-all (= 3.11.4-5),
python3-all-dev (= 3.11.4-5),
python3-appdirs (= 1.4.4-4),
python3-attr (= 23.1.0-2),
python3-babel (= 2.10.3-2),
python3-brotli (= 1.0.9-2+b3),
python3-certifi (= 2023.7.22-1),
python3-chardet (= 5.2.0+dfsg-1),
python3-charset-normalizer (= 3.3.0-1),
python3-contourpy (= 1.0.7-1),
python3-cycler (= 0.11.0-1),
python3-dateutil (= 2.8.2-3),
python3-decorator (= 5.1.1-5),
python3-dev (= 3.11.4-5),
python3-distutils (= 3.11.5-1),
python3-docutils (= 0.19+dfsg-8),
python3-fonttools (= 4.38.0-1),
python3-fs (= 2.4.16-2),
python3-idna (= 3.3-2),
python3-imagesize (= 1.4.1-1),
python3-iniconfig (= 1.1.1-2),
python3-jinja2 (= 3.1.2-1),
python3-kiwisolver (= 1.4.4-1),
python3-lib2to3 (= 3.11.5-1),
python3-lxml (= 4.9.3-1),
python3-lz4 (= 4.0.2+dfsg-1+b1),
python3-markupsafe (= 2.1.3-1),
python3-matplotlib (= 3.6.3-1),
python3-minimal (= 3.11.4-5),
python3-mpmath (= 1.2.1-2),
python3-numpy (= 1:1.24.2-1),
python3-numpydoc (= 1.5.0-1),
python3-packaging (= 23.1-1),
python3-pandas (= 1.5.3+dfsg-6),
python3-pandas-lib (= 1.5.3+dfsg-6),
python3-pil (= 10.0.0-1),
python3-pil.imagetk (= 10.0.0-1),
python3-pkg-resources (= 68.1.2-2),
python3-pluggy (= 1.3.0-1),
python3-psutil (= 5.9.5-1),
python3-pygments (= 2.15.1+dfsg-1),
python3-pyparsing (= 3.1.1-1),
python3-pysam (= 0.20.0+ds-3+rpi1),
python3-pytest (= 7.4.3-1),
python3-requests (= 2.31.0+dfsg-1),
python3-roman (= 3.3-3),
python3-scipy (= 1.10.1-2+rpi1),
python3-setuptools (= 68.1.2-2),
python3-six (= 1.16.0-4),
python3-snowballstemmer (= 2.2.0-4),
python3-sphinx (= 5.3.0-7),
python3-sympy (= 1.12-6),
python3-tk (= 3.11.5-1),
python3-tz (= 2023.3.post1-1),
python3-ufolib2 (= 0.16.0+dfsg1-1),
python3-urllib3 (= 1.26.18-1),
python3-yaml (= 6.0.1-1),
python3.11 (= 3.11.6-3),
python3.11-dev (= 3.11.6-3),
python3.11-minimal (= 3.11.6-3),
r-base-core (= 4.3.2-1),
readline-common (= 8.2-1.3),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sgml-base (= 1.31),
sphinx-common (= 5.3.0-7),
sysvinit-utils (= 3.08-3),
tar (= 1.34+dfsg-1.2),
tk8.6-blt2.5 (= 2.5.3+dfsg-4.1),
tzdata (= 2023c-10),
ucf (= 3.0043+nmu1),
unicode-data (= 15.1.0-1),
unzip (= 6.0-28),
usr-is-merged (= 37),
util-linux (= 2.39.2-5),
x11-common (= 1:7.7+23),
xdg-utils (= 1.1.3-4.1),
xml-core (= 0.18+nmu1),
xz-utils (= 5.4.4-0.1),
zip (= 3.0-13),
zlib1g (= 1:1.2.13.dfsg-3),
zlib1g-dev (= 1:1.2.13.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1698410126"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
python3-pybedtools-dbgsym_0.9.1-1_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 1114964 bytes: control archive=656 bytes.
455 bytes, 12 lines control
310 bytes, 3 lines md5sums
Package: python3-pybedtools-dbgsym
Source: python-pybedtools
Version: 0.9.1-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1190
Depends: python3-pybedtools (= 0.9.1-1)
Section: debug
Priority: optional
Description: debug symbols for python3-pybedtools
Build-Ids: 0bb12e8a1faac55714f762f881bd67fb942a7650 d45da17e5665331d6912ac7e401d795251996849
drwxr-xr-x root/root 0 2023-10-27 12:35 ./
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/lib/
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/lib/debug/
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/lib/debug/.build-id/0b/
-rw-r--r-- root/root 735044 2023-10-27 12:35 ./usr/lib/debug/.build-id/0b/b12e8a1faac55714f762f881bd67fb942a7650.debug
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/lib/debug/.build-id/d4/
-rw-r--r-- root/root 365096 2023-10-27 12:35 ./usr/lib/debug/.build-id/d4/5da17e5665331d6912ac7e401d795251996849.debug
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 103704 2023-10-27 12:35 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/python3-pybedtools.debug
drwxr-xr-x root/root 0 2023-10-27 12:35 ./usr/share/
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python3-pybedtools_0.9.1-1_armhf.deb
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new Debian package, version 2.0.
size 12142912 bytes: control archive=4544 bytes.
803 bytes, 17 lines control
12902 bytes, 132 lines md5sums
283 bytes, 12 lines * postinst #!/bin/sh
396 bytes, 12 lines * prerm #!/bin/sh
Package: python3-pybedtools
Source: python-pybedtools
Version: 0.9.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 17079
Depends: python3 (<< 3.12), python3 (>= 3.11~), python3-numpy, python3-pysam, python3-six, python3:any, libc6 (>= 2.33), libgcc-s1 (>= 3.5), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4)
Suggests: python-pybedtools-doc
Section: python
Priority: optional
Homepage: https://daler.github.io/pybedtools/
Description: Python 3 wrapper around BEDTools for bioinformatics work
The BEDTools suite of programs is widely used for genomic interval
manipulation or “genome algebra”. pybedtools wraps and extends BEDTools and
offers feature-level manipulations from within Python.
.
This is the Python 3 version.
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Build Architecture: armhf
Build Type: any
Build-Space: 151884
Build-Time: 146
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 160
Job: python-pybedtools_0.9.1-1
Machine Architecture: arm64
Package: python-pybedtools
Package-Time: 315
Source-Version: 0.9.1-1
Space: 151884
Status: successful
Version: 0.9.1-1
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Finished at 2023-11-06T05:09:55Z
Build needed 00:05:15, 151884k disk space