Wed Dec 25 09:44:48 UTC 2024 I: starting to build python-pybedtools/unstable/amd64 on jenkins on '2024-12-25 09:44' Wed Dec 25 09:44:48 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_29/29313/console.log Wed Dec 25 09:44:48 UTC 2024 I: Downloading source for unstable/python-pybedtools=0.10.0-3 --2024-12-25 09:44:48-- http://deb.debian.org/debian/pool/main/p/python-pybedtools/python-pybedtools_0.10.0-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2527 (2.5K) [text/prs.lines.tag] Saving to: ‘python-pybedtools_0.10.0-3.dsc’ 0K .. 100% 387M=0s 2024-12-25 09:44:48 (387 MB/s) - ‘python-pybedtools_0.10.0-3.dsc’ saved [2527/2527] Wed Dec 25 09:44:48 UTC 2024 I: python-pybedtools_0.10.0-3.dsc -----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: 0.10.0-3 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Steffen Moeller 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: 8636fa6a2d680b715f7ef1bb42aa45db109d854c 12032584 python-pybedtools_0.10.0.orig.tar.xz 8740e43c649f1d2302626041f3cf656a538f03f7 31140 python-pybedtools_0.10.0-3.debian.tar.xz Checksums-Sha256: 8b72ddd6dac632c3622848189f53787221b92c71a6f8ff0f802401135a3b6be7 12032584 python-pybedtools_0.10.0.orig.tar.xz 34db52b71620f8b05be7c4a6495dfc445890a38eb1a8a9ca5bb59369ec2d78e6 31140 python-pybedtools_0.10.0-3.debian.tar.xz Files: 602c5d35b956f4c3b5e736f13731d564 12032584 python-pybedtools_0.10.0.orig.tar.xz e6f9f0fc0f19214c2bcacb5b17ad5b96 31140 python-pybedtools_0.10.0-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEE3lnVbvHK7ir4q61+p3sXeEcY/EFAmdrPokSHGVhbWFudUBk ZWJpYW4ub3JnAAoJEPqd7F3hHGPxolYP/22SeP+EGAq7wNQoWJPrz62E8DdiFbC9 ADOUu86+6vlAxBs6uzAl2Pc2zdWl5dI2eSuX056ciUE57wqLQ4iN5VTZXDoD/DIR zLO+AAaLtg3WmCdr0H7BYi99tG12Sk2Zd41SohbS/C2TcMOFtDGUX8zqq73yGkLZ 2IWKbE2xfvygY6LI3l6Jz0SyPRBWkP27bYyO7t+FcLaZJ+x7mOxG8WnWiSdPhPGc dJZeg4ByDcTL4902cwrDrpHSvtP+B4HEyWy2bR9Yc+zvrNWg7G8XgssyNcs73fGF 6PJhM2v+AYiU1eIPRhNlPJ63GqROiHRlfIqzrd5dDlhz45naea2xUOyTPxKPxZbP rUChfaUBAlvq5/A0G8umWlxbAD/qGvk2rhGfOon685sQhFNFX5oudYTAAW+2b+E5 qyLn80CK/mglxCddbiFlDNOIALOJKvDDOOPQ8eeXf+Y5ZyjU2gOQI4f4wyJJMdKC CvD+btOeoejOCIDdb2luJ64mZwo7bd0slQoEMDhk5j4obo5S4zzy+SlO+3mZEOgs +XgB490jyndEsPsgkoomJ8MHZgwlnL1s5UFuQrn43mb5QMLF/Yl0V1/qyQ8FLVhD 7UU1N1/uiolvKoRbimaZCVVcr3ZJot65iBJIfOqdMrGZFwvWCvzVVUubRBg3Ejsd kG4nTmzDEo1J =AUV9 -----END PGP SIGNATURE----- Wed Dec 25 09:44:48 UTC 2024 I: Checking whether the package is not for us Wed Dec 25 09:44:48 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Wed Dec 25 09:44:48 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Wed Dec 25 10:58:46 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 24 21:44:51 -12 2024 I: pbuilder-time-stamp: 1735119891 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-pybedtools_0.10.0-3.dsc] I: copying [./python-pybedtools_0.10.0.orig.tar.xz] I: copying [./python-pybedtools_0.10.0-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.10.0-3.dsc: unsupported subcommand dpkg-source: info: extracting python-pybedtools in python-pybedtools-0.10.0 dpkg-source: info: unpacking python-pybedtools_0.10.0.orig.tar.xz dpkg-source: info: unpacking python-pybedtools_0.10.0-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying define_filenotfounderror_python2.patch dpkg-source: info: applying remove_badges_from_documentation.patch dpkg-source: info: applying add_missing_shebang.patch dpkg-source: info: applying yaml_safe_load.patch dpkg-source: info: applying 416.patch dpkg-source: info: applying fix-doctest-imports.py I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/737479/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='f8fc1920861144fbba751f90d84d9796' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='737479' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.56Cy3Wgr/pbuilderrc_T03i --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.56Cy3Wgr/b1 --logfile b1/build.log python-pybedtools_0.10.0-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/737479/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, 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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19857 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on bedtools; however: Package bedtools is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam; however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-numpydoc; however: Package python3-numpydoc is not installed. pbuilder-satisfydepends-dummy depends on python3-pandas; however: Package python3-pandas is not installed. pbuilder-satisfydepends-dummy depends on python3-psutil; however: Package python3-psutil is not installed. pbuilder-satisfydepends-dummy depends on python3-yaml; however: Package python3-yaml is not installed. pbuilder-satisfydepends-dummy depends on python3-tk; however: Package python3-tk is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bedtools{a} blt{a} bsdextrautils{a} ca-certificates{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lyx{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgcrypt20{a} libgfortran5{a} libglib2.0-0t64{a} libgnutls30t64{a} libgpg-error0{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libidn2-0{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libopenjp2-7{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{a} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libtasn1-6{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxslt1.1{a} libxss1{a} libxt6t64{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} openssl{a} po-debconf{a} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-brotli{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-fonttools{a} python3-fs{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-psutil{a} python3-pygments{a} python3-pyparsing{a} python3-pysam{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sympy{a} python3-tabulate{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} r-base-core{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} tzdata{a} ucf{a} unicode-data{a} unzip{a} x11-common{a} xdg-utils{a} xml-core{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpg-error-l10n libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-numba python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-tables r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 240 newly installed, 0 to remove and 0 not upgraded. Need to get 187 MB of archives. After unpacking 795 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.8-3 [2162 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.8-1 [26.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 13 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.8-3 [677 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.8-1 [9788 B] Get: 23 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.8-1 [27.9 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-2 [858 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-2 [2198 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20241223 [164 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-3 [200 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0046 [41.1 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-3 [723 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b3 [27.8 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b3 [54.6 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 69 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-1+b1 [3157 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.22 [90.5 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 76 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-3 [1600 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.22 [919 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 91 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.6.0-1 [720 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241217 [113 kB] Get: 97 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.19+dfsg-1 [187 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-11 [836 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.4-1 [1501 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 133 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-3 [30.4 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 146 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3 [16.3 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3 [16.1 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.8-3 [2154 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.8-3 [5134 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.8-1 [10.1 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-2 [1975 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.1-2 [2151 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.1-2 [5009 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.8-1 [1068 B] Get: 163 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 165 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-2 [740 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.8-1 [1048 B] Get: 179 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.8-3 [505 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.8-1 [26.1 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.1-2 [504 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.8-1 [1068 B] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.16.0-1 [114 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 187 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 python3-contourpy amd64 1.3.1-1 [264 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 192 http://deb.debian.org/debian unstable/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 python3-tz all 2024.2-1 [31.0 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 python3-fs all 2.4.16-5.1 [95.2 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 python3-lz4 amd64 4.4.0+dfsg-1 [25.5 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 python3-scipy amd64 1.14.1-3 [20.5 MB] Get: 203 http://deb.debian.org/debian unstable/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 python3-fonttools amd64 4.55.0-3 [1634 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 210 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 211 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1.1 [120 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 python3.12-tk amd64 3.12.8-3 [113 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 python3.13-tk amd64 3.13.1-2 [103 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 python3-tk amd64 3.13.1-1 [9464 B] Get: 218 http://deb.debian.org/debian unstable/main amd64 python3-pil.imagetk amd64 10.4.0-1+b1 [79.8 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-3 [617 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.2.3-4 [112 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-3 [468 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 python3-numpydoc all 1.8.0-1 [51.4 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5+b1 [7307 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-14 [233 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-28 [166 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Fetched 187 MB in 12s (15.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19857 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../16-libpython3.12-stdlib_3.12.8-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../17-python3.12_3.12.8-3_amd64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.2.1-1) ... Setting up unzip (6.0-28) ... Setting up libdebhelper-perl (13.22) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libcom-err2:amd64 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up python-babel-localedata (2.16.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Dec 25 09:50:02 UTC 2024. Universal Time is now: Wed Dec 25 09:50:02 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libpython3.13-minimal:amd64 (3.13.1-2) ... Setting up zip (3.0-14) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libfribidi0:amd64 (1.0.16-1) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up libunistring5:amd64 (1.3-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-3) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up autopoint (0.22.5-3) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-11) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.4.6-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up libjson-perl (4.10000-1) ... Setting up libtasn1-6:amd64 (4.19.0-3+b3) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up python3.13-minimal (3.13.1-2) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libpaper2:amd64 (2.2.5-0.3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up bedtools (2.31.1+dfsg-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-3) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b3) ... Setting up libtool (2.4.7-8) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... Setting up libpaper-utils (2.2.5-0.3) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 152 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.82.4-1) ... No schema files found: doing nothing. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up ucf (3.0046) ... Setting up libjs-sphinxdoc (8.1.3-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libharfbuzz0b:amd64 (10.1.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-2) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libpython3.13:amd64 (3.13.1-2) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b3) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up python3.13 (3.13.1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libpango-1.0-0:amd64 (1.55.0+ds-3) ... Setting up python3.12-tk (3.12.8-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.1-2) ... Setting up libldap-2.5-0:amd64 (2.5.19+dfsg-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up libpython3.13-dev:amd64 (3.13.1-2) ... Setting up sphinx-common (8.1.3-3) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up libpangocairo-1.0-0:amd64 (1.55.0+ds-3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-3) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... Setting up python3.13-dev (3.13.1-2) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.8-3) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ... Setting up debhelper (13.22) ... Setting up libpython3.12t64:amd64 (3.12.8-3) ... Setting up r-base-core (4.4.2-1) ... Creating config file /etc/R/Renviron with new version Setting up libhts3t64:amd64 (1.20+ds-2) ... Setting up libpython3-stdlib:amd64 (3.12.8-1) ... Setting up python3 (3.12.8-1) ... Setting up libpython3.12-dev:amd64 (3.12.8-3) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-psutil (5.9.8-2) ... Setting up python3-tz (2024.2-1) ... Setting up python3-pil:amd64 (10.4.0-1+b1) ... Setting up python3-roman (4.2-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-jinja2 (3.1.3-1.1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.8-3) ... Setting up cython3 (3.0.11+dfsg-1+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-urllib3 (2.2.3-4) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-lxml:amd64 (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-pysam (0.22.1+ds-2+b2) ... Setting up libpython3-dev:amd64 (3.12.8-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.4.0+dfsg-1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-pytest (8.3.4-1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-tabulate (0.9.0-1) ... Setting up python3-all (3.12.8-1) ... Setting up python3-yaml (6.0.2-1+b1) ... Setting up python3-tk:amd64 (3.13.1-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Setting up libpython3-all-dev:amd64 (3.12.8-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.8-1) ... Setting up python3-pkg-resources (75.6.0-1) ... Setting up python3-all-dev (3.12.8-1) ... Setting up python3-setuptools (75.6.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-fs (2.4.16-5.1) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-contourpy (1.3.1-1) ... Setting up dh-python (6.20241217) ... Setting up python3-scipy (1.14.1-3) ... Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5+b1) ... Setting up python3-pandas (2.2.3+dfsg-5) ... Setting up python3-fonttools (4.55.0-3) ... Setting up python3-ufolib2 (0.17.0+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-3) ... Setting up python3-numpydoc (1.8.0-1) ... Processing triggers for ca-certificates (20241223) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-pybedtools-0.10.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pybedtools_0.10.0-3_source.changes dpkg-buildpackage: info: source package python-pybedtools dpkg-buildpackage: info: source version 0.10.0-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Emmanuel Arias dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 dpkg-source: info: using options from python-pybedtools-0.10.0/debian/source/options: --extend-diff-ignore=(pybedtools/version.py|docs/source/pybedtools.featurefuncs.*.rst) debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0' /bin/rm -rf fakehome .eggs .pybuild .pytest_cache /bin/rm -rf debian/python3-pybedtools debian/files /bin/rm -rf pybedtools.egg-info /bin/rm -rf pybedtools/scripts/__pycache__/ /bin/rm -rf pybedtools/contrib/__pycache__/ /bin/rm -rf pybedtools/__pycache__/ find pybedtools -name "*.so" -o -name "*.o" | xargs -r rm rm -rf build rm -rf docs/build docs/*.bed docs/*.genome rm -rf dist /bin/rm -rf pybedtools/cbedtools.cpp pybedtools/featurefuncs.cpp find docs/source/autodocs/ -name "*.rst" | xargs -r /bin/rm # dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running config I: pybuild base:311: python3.12 setup.py config /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0' python3 setup.py cythonize /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running cythonize /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/cbedtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) Compiling pybedtools/cbedtools.pyx because it changed. Compiling pybedtools/featurefuncs.pyx because it changed. [1/2] Cythonizing pybedtools/cbedtools.pyx [2/2] Cythonizing pybedtools/featurefuncs.pyx dh_auto_build I: pybuild base:311: /usr/bin/python3.13 setup.py build /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running build running build_py creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/stats.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/logger.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/paths.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/genome_registry.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/version.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/parallel.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/bedtool.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/filenames.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/settings.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_gzip_support.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_iter.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_pathlib.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_contrib.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/tfuncs.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/regression_tests.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/genomepy_integration.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_len_leak.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_1.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_issues.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_cbedtools.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/plotting.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data running egg_info creating pybedtools.egg-info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt writing manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'pybedtools' warning: no previously-included files matching '__pycache__' found under directory '*' warning: no previously-included files matching '*.py[co]' found under directory '*' adding license file 'LICENSE.txt' writing manifest file 'pybedtools.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/_Window.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/cbedtools.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/cbedtools.pxd -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/cbedtools.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/featurefuncs.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/featurefuncs.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/bedFile.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/bedFile.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/fileType.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/fileType.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/gzstream.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/gzstream.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/lineFileUtilities.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/1000genomes-example.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg38-problem.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/v.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/y.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/small.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/small.fastq -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/c.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue_121.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.cram -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/tag_test1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/164.gtf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/bedpe2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/expand_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/mm9.bed12 -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/d.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/x.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/exons.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/x.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/m1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/venn.b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/example.narrowPeak -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/tag_test2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/reads.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/genome.fa -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.vcf.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test.fa -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_tsses.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.links.html -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.out.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/democonfig.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/gchart-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/mpl-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/prevent_open_file_regression -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_cases.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_merge215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_merge227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_shuffle215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_shuffle227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test running build_ext building 'pybedtools.cbedtools' extension creating build/temp.linux-x86_64-cpython-313/pybedtools creating build/temp.linux-x86_64-cpython-313/pybedtools/include x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/cbedtools.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/bedFile.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/fileType.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/gzstream.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-313/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-313/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/cbedtools.cpython-313-x86_64-linux-gnu.so building 'pybedtools.featurefuncs' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/featurefuncs.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/featurefuncs.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/bedFile.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/fileType.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-313/pybedtools/include/gzstream.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-313/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-313/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/featurefuncs.cpython-313-x86_64-linux-gnu.so I: pybuild base:311: /usr/bin/python3 setup.py build /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running build running build_py creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/stats.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/logger.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/paths.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/genome_registry.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/version.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/parallel.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/bedtool.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/filenames.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/settings.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_gzip_support.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_iter.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_pathlib.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_contrib.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/tfuncs.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/regression_tests.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/genomepy_integration.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_len_leak.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_1.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_issues.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_cbedtools.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/plotting.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data running egg_info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt reading manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'pybedtools' warning: no previously-included files matching '__pycache__' found under directory '*' warning: no previously-included files matching '*.py[co]' found under directory '*' adding license file 'LICENSE.txt' writing manifest file 'pybedtools.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/_Window.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/cbedtools.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/cbedtools.pxd -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/cbedtools.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/featurefuncs.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/featurefuncs.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/bedFile.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/bedFile.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/fileType.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/fileType.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/gzstream.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/gzstream.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/lineFileUtilities.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/1000genomes-example.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg38-problem.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/v.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/y.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/small.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/small.fastq -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/c.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue_121.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.cram -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/tag_test1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/164.gtf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/bedpe2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/expand_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/mm9.bed12 -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/d.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/x.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/exons.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/x.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/m1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/venn.b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/example.narrowPeak -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/tag_test2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/reads.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/genome.fa -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.vcf.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test.fa -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_tsses.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.links.html -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.out.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/democonfig.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/gchart-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/mpl-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/prevent_open_file_regression -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_cases.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_merge215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_merge227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_shuffle215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_shuffle227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test running build_ext building 'pybedtools.cbedtools' extension creating build/temp.linux-x86_64-cpython-312/pybedtools creating build/temp.linux-x86_64-cpython-312/pybedtools/include x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/cbedtools.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so building 'pybedtools.featurefuncs' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/featurefuncs.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/featurefuncs.cpython-312-x86_64-linux-gnu.so python3 setup.py develop --user /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running develop /usr/lib/python3/dist-packages/setuptools/command/develop.py:41: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! easy_install.initialize_options(self) /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running egg_info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt reading manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'pybedtools' warning: no previously-included files matching '__pycache__' found under directory '*' warning: no previously-included files matching '*.py[co]' found under directory '*' adding license file 'LICENSE.txt' writing manifest file 'pybedtools.egg-info/SOURCES.txt' running build_ext building 'pybedtools.cbedtools' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/cbedtools.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so building 'pybedtools.featurefuncs' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/featurefuncs.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/featurefuncs.cpython-312-x86_64-linux-gnu.so Creating /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/lib/python3.12/site-packages/pybedtools.egg-link (link to .) Adding pybedtools 0.10.0 to easy-install.pth file Installed /build/reproducible-path/python-pybedtools-0.10.0 Processing dependencies for pybedtools==0.10.0 Searching for pysam==0.22.1 Best match: pysam 0.22.1 Adding pysam 0.22.1 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for numpy==1.26.4 Best match: numpy 1.26.4 Adding numpy 1.26.4 to easy-install.pth file Installing f2py script to /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/bin Installing f2py3 script to /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/bin Installing f2py3.13 script to /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/bin Installing f2py3.12 script to /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/bin Using /usr/lib/python3/dist-packages Finished processing dependencies for pybedtools==0.10.0 sphinx-build -N -b html docs/source docs/html Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst [autosummary] generating autosummary for: /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.add_color.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.extend_fields.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.five_prime.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.greater_than.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.less_than.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.three_prime.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 48 source files that are out of date updating environment: [new config] 157 added, 0 changed, 0 removed reading sources... [ 1%] 3-brief-examples reading sources... [ 1%] FAQs reading sources... [ 2%] autodoc_source /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/contrib/long_range_interaction.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.annotate reading sources... [ 5%] autodocs/pybedtools.bedtool.BedTool.any_hits reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.at reading sources... [ 7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bed6 reading sources... [ 9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize reading sources... 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[100%] tutorial-contents /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history..decorated:9: WARNING: Lexing literal_block 'Tool: bedtools expand \nVersion: v2.31.1\nSummary: Replicate lines in a file based on columns of comma-separated values.\n\nUsage: bedtools expand -c [COLS] \nOptions: \n -i Input file. Assumes "stdin" if omitted.\n\n -c Specify the column (1-based) that should be summarized.\n - Required.\nExamples: \n $ cat test.txt\n chr1 10 20 1,2,3 10,20,30\n chr1 40 50 4,5,6 40,50,60\n\n $ bedtools expand test.txt -c 5\n chr1 10 20 1,2,3 10\n chr1 10 20 1,2,3 20\n chr1 10 20 1,2,3 30\n chr1 40 50 4,5,6 40\n chr1 40 50 4,5,6 50\n chr1 40 50 4,5,6 60\n\n $ bedtools expand test.txt -c 4,5\n chr1 10 20 1 10\n chr1 10 20 2 20\n chr1 10 20 3 30\n chr1 40 50 4 40\n chr1 40 50 5 50\n chr1 40 50 6 60' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history..decorated:28: WARNING: Lexing literal_block 'Tool: bedtools groupby \nVersion: v2.31.1\nSummary: Summarizes a dataset column based upon\n common column groupings. Akin to the SQL "group by" command.\n\nUsage: bedtools groupby -g [group**column(s)] -c [op**column(s)] -o [ops] \n cat [FILE] | bedtools groupby -g [group**column(s)] -c [op**column(s)] -o [ops] \n\nOptions: \n -i Input file. Assumes "stdin" if omitted.\n\n -g -grp Specify the columns (1-based) for the grouping.\n The columns must be comma separated.\n - Default: 1,2,3\n\n -c -opCols Specify the column (1-based) that should be summarized.\n - Required.\n\n -o -ops Specify the operation that should be applied to opCol.\n Valid operations:\n sum, count, count**distinct, min, max,\n mean, median, mode, antimode,\n stdev, sstdev (sample standard dev.),\n collapse (i.e., print a comma separated list (duplicates allowed)), \n distinct (i.e., print a comma separated list (NO duplicates allowed)), \n distinct**sort**num (as distinct, but sorted numerically, ascending), \n distinct**sort**num**desc (as distinct, but sorted numerically, descending), \n concat (i.e., merge values into a single, non-delimited string), \n freqdesc (i.e., print desc. list of values:freq)\n freqasc (i.e., print asc. list of values:freq)\n first (i.e., print first value)\n last (i.e., print last value)\n - Default: sum\n\n If there is only column, but multiple operations, all operations will be\n applied on that column. Likewise, if there is only one operation, but\n multiple columns, that operation will be applied to all columns.\n Otherwise, the number of columns must match the the number of operations,\n and will be applied in respective order.\n E.g., "-c 5,4,6 -o sum,mean,count" will give the sum of column 5,\n the mean of column 4, and the count of column 6.\n The order of output columns will match the ordering given in the command.\n\n -full Print all columns from input file. The first line in the group is used.\n Default: print only grouped columns.\n\n -inheader Input file has a header line - the first line will be ignored.\n\n -outheader Print header line in the output, detailing the column names. \n If the input file has headers (-inheader), the output file\n will use the input\'s column names.\n If the input file has no headers, the output file\n will use "col**1", "col**2", etc. as the column names.\n\n -header same as \'-inheader -outheader\'\n\n -ignorecase Group values regardless of upper/lower case.\n\n -prec Sets the decimal precision for output (Default: 5)\n\n -delim Specify a custom delimiter for the collapse operations.\n - Example: -delim "|"\n - Default: ",".\n\nExamples: \n $ cat ex1.out\n chr1 10 20 A chr1 15 25 B.1 1000 ATAT\n chr1 10 20 A chr1 25 35 B.2 10000 CGCG\n\n $ groupBy -i ex1.out -g 1,2,3,4 -c 9 -o sum\n chr1 10 20 A 11000\n\n $ groupBy -i ex1.out -grp 1,2,3,4 -opCols 9,9 -ops sum,max\n chr1 10 20 A 11000 10000\n\n $ groupBy -i ex1.out -g 1,2,3,4 -c 8,9 -o collapse,mean\n chr1 10 20 A B.1,B.2, 5500\n\n $ cat ex1.out | groupBy -g 1,2,3,4 -c 8,9 -o collapse,mean\n chr1 10 20 A B.1,B.2, 5500\n\n $ cat ex1.out | groupBy -g 1,2,3,4 -c 10 -o concat\n chr1 10 20 A ATATCGCG\n\nNotes: \n (1) The input file/stream should be sorted/grouped by the -grp. columns\n (2) If -i is unspecified, input is assumed to come from stdin.' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history..decorated:20: WARNING: Lexing literal_block 'Tool: bedtools overlap (aka getOverlap)\nVersion: v2.31.1\nSummary: Computes the amount of overlap (positive values)\n or distance (negative values) between genome features\n and reports the result at the end of the same line.\n\nOptions: \n -i Input file. Use "stdin" for pipes.\n\n -cols Specify the columns (1-based) for the starts and ends of the\n features for which you\'d like to compute the overlap/distance.\n The columns must be listed in the following order: \n\n start1,end1,start2,end2\n\nExample: \n $ bedtools window -a A.bed -b B.bed -w 10\n chr1 10 20 A chr1 15 25 B\n chr1 10 20 C chr1 25 35 D\n\n $ bedtools window -a A.bed -b B.bed -w 10 | bedtools overlap -i stdin -cols 2,3,6,7\n chr1 10 20 A chr1 15 25 B 5\n chr1 10 20 C chr1 25 35 D -5' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history..decorated:16: WARNING: Lexing literal_block 'Tool: bedtools makewindows\nVersion: v2.31.1\nSummary: Makes adjacent or sliding windows across a genome or BED file.\n\nUsage: bedtools makewindows [OPTIONS] [-g OR -b ]\n [ -w OR -n ]\n\nInput Options: \n -g \n Genome file size (see notes below).\n Windows will be created for each chromosome in the file.\n\n -b \n BED file (with chrom,start,end fields).\n Windows will be created for each interval in the file.\n\nWindows Output Options: \n -w \n Divide each input interval (either a chromosome or a BED interval)\n to fixed-sized windows (i.e. same number of nucleotide in each window).\n Can be combined with -s \n\n -s \n Step size: i.e., how many base pairs to step before\n creating a new window. Used to create "sliding" windows.\n - Defaults to window size (non-sliding windows).\n\n -n \n Divide each input interval (either a chromosome or a BED interval)\n to fixed number of windows (i.e. same number of windows, with\n varying window sizes).\n\n -reverse\n Reverse numbering of windows in the output, i.e. report \n windows in decreasing order\n\nID Naming Options: \n -i src|winnum|srcwinnum\n The default output is 3 columns: chrom, start, end .\n With this option, a name column will be added.\n "-i src" - use the source interval\'s name.\n "-i winnum" - use the window number as the ID (e.g. 1,2,3,4...).\n "-i srcwinnum" - use the source interval\'s name with the window number.\n See below for usage examples.\n\nNotes: \n (1) The genome file should tab delimited and structured as follows:\n \n\n For example, Human (hg19):\n chr1 249250621\n chr2 243199373\n ...\n chr18**gl000207**random 4262\n\nTip 1. Use samtools faidx to create a genome file from a FASTA: \n One can the samtools faidx command to index a FASTA file.\n The resulting .fai index is suitable as a genome file, \n as bedtools will only look at the first two, relevant columns\n of the .fai file.\n\n For example:\n samtools faidx GRCh38.fa\n bedtools makewindows -w 100 -g GRCh38.fa.fai\n\nTip 2. Use UCSC Table Browser to create a genome file: \n One can use the UCSC Genome Browser\'s MySQL database to extract\n chromosome sizes. For example, H. sapiens:\n\n mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\\n "select chrom, size from hg19.chromInfo" > hg19.genome\n\nExamples: \n # Divide the human genome into windows of 1MB:\n $ bedtools makewindows -g hg19.txt -w 1000000\n chr1 0 1000000\n chr1 1000000 2000000\n chr1 2000000 3000000\n chr1 3000000 4000000\n chr1 4000000 5000000\n ...\n\n # Divide the human genome into sliding (=overlapping) windows of 1MB, with 500KB overlap:\n $ bedtools makewindows -g hg19.txt -w 1000000 -s 500000\n chr1 0 1000000\n chr1 500000 1500000\n chr1 1000000 2000000\n chr1 1500000 2500000\n chr1 2000000 3000000\n ...\n\n # Divide each chromosome in human genome to 1000 windows of equal size:\n $ bedtools makewindows -g hg19.txt -n 1000\n chr1 0 249251\n chr1 249251 498502\n chr1 498502 747753\n chr1 747753 997004\n chr1 997004 1246255\n ...\n\n # Divide each interval in the given BED file into 10 equal-sized windows:\n $ cat input.bed\n chr5 60000 70000\n chr5 73000 90000\n chr5 100000 101000\n $ bedtools makewindows -b input.bed -n 10\n chr5 60000 61000\n chr5 61000 62000\n chr5 62000 63000\n chr5 63000 64000\n chr5 64000 65000\n ...\n\n # Add a name column, based on the window number: \n $ cat input.bed\n chr5 60000 70000 AAA\n chr5 73000 90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i winnum\n chr5 60000 63334 1\n chr5 63334 66668 2\n chr5 66668 70000 3\n chr5 73000 78667 1\n chr5 78667 84334 2\n chr5 84334 90000 3\n chr5 100000 100334 1\n chr5 100334 100668 2\n chr5 100668 101000 3\n ...\n\n # Reverse window numbers: \n $ cat input.bed\n chr5 60000 70000 AAA\n chr5 73000 90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i winnum -reverse\n chr5 60000 63334 3\n chr5 63334 66668 2\n chr5 66668 70000 1\n chr5 73000 78667 3\n chr5 78667 84334 2\n chr5 84334 90000 1\n chr5 100000 100334 3\n chr5 100334 100668 2\n chr5 100668 101000 1\n ...\n\n # Add a name column, based on the source ID + window number: \n $ cat input.bed\n chr5 60000 70000 AAA\n chr5 73000 90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i srcwinnum\n chr5 60000 63334 AAA**1\n chr5 63334 66668 AAA**2\n chr5 66668 70000 AAA**3\n chr5 73000 78667 BBB**1\n chr5 78667 84334 BBB**2\n chr5 84334 90000 BBB**3\n chr5 100000 100334 CCC**1\n chr5 100334 100668 CCC**2\n chr5 100668 101000 CCC**3\n ...' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/default-arguments.rst:35: WARNING: Lexing literal_block '$ intersectBed -a a.bed -b b.bed -u > tmpfile' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-design-principles.rst:120: WARNING: unknown option: 'mergeBed -i' [ref.option] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-design-principles.rst:127: WARNING: unknown option: '-i' [ref.option] generating indices... genindex py-modindex done highlighting module code... [ 8%] pybedtools highlighting module code... [ 15%] pybedtools.bedtool highlighting module code... [ 23%] pybedtools.cbedtools highlighting module code... [ 31%] pybedtools.contrib.bigbed highlighting module code... [ 38%] pybedtools.contrib.bigwig highlighting module code... 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The HTML pages are in docs/html. make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp /build/reproducible-path/python-pybedtools-0.10.0/debian/mpl-expected.png /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/ ; python3 /build/reproducible-path/python-pybedtools-0.10.0/setup.py install --user ; export HOME=/build/reproducible-path/python-pybedtools-0.10.0/fakehome /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() running bdist_egg running egg_info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt reading manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'pybedtools' 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' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/logger.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/paths.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/version.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/parallel.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/helpers.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/bedtool.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-312/pybedtools creating build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_pathlib.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_1.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_issues.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test creating build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib creating build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/_Window.pyx -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/cbedtools.cpp -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/cbedtools.pxd -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/cbedtools.pyx -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/featurefuncs.cpp -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/featurefuncs.pyx -> build/lib.linux-x86_64-cpython-312/pybedtools creating build/lib.linux-x86_64-cpython-312/pybedtools/include copying pybedtools/include/bedFile.cpp -> build/lib.linux-x86_64-cpython-312/pybedtools/include copying pybedtools/include/bedFile.h -> build/lib.linux-x86_64-cpython-312/pybedtools/include copying pybedtools/include/fileType.cpp -> build/lib.linux-x86_64-cpython-312/pybedtools/include copying pybedtools/include/fileType.h -> build/lib.linux-x86_64-cpython-312/pybedtools/include copying pybedtools/include/gzstream.cpp -> build/lib.linux-x86_64-cpython-312/pybedtools/include copying pybedtools/include/gzstream.h -> build/lib.linux-x86_64-cpython-312/pybedtools/include copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-x86_64-cpython-312/pybedtools/include copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue319.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/genome.fa -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/gchart-expected.png -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/mpl-expected.png -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_cases.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_merge215.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_merge227.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-x86_64-cpython-312/pybedtools/test running build_ext building 'pybedtools.cbedtools' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/cbedtools.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so building 'pybedtools.featurefuncs' extension x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/featurefuncs.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-312/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-312/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o build/lib.linux-x86_64-cpython-312/pybedtools/featurefuncs.cpython-312-x86_64-linux-gnu.so creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/stats.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/featurefuncs.cpp -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/_Window.pyx -> build/bdist.linux-x86_64/egg/pybedtools creating build/bdist.linux-x86_64/egg/pybedtools/include copying build/lib.linux-x86_64-cpython-312/pybedtools/include/bedFile.h -> build/bdist.linux-x86_64/egg/pybedtools/include copying build/lib.linux-x86_64-cpython-312/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-x86_64/egg/pybedtools/include copying build/lib.linux-x86_64-cpython-312/pybedtools/include/fileType.h -> build/bdist.linux-x86_64/egg/pybedtools/include copying build/lib.linux-x86_64-cpython-312/pybedtools/include/gzstream.cpp -> build/bdist.linux-x86_64/egg/pybedtools/include copying build/lib.linux-x86_64-cpython-312/pybedtools/include/bedFile.cpp -> build/bdist.linux-x86_64/egg/pybedtools/include copying build/lib.linux-x86_64-cpython-312/pybedtools/include/gzstream.h -> build/bdist.linux-x86_64/egg/pybedtools/include copying build/lib.linux-x86_64-cpython-312/pybedtools/include/fileType.cpp -> build/bdist.linux-x86_64/egg/pybedtools/include copying build/lib.linux-x86_64-cpython-312/pybedtools/logger.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/paths.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.pyx -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/genome_registry.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/version.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/__init__.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/parallel.py -> build/bdist.linux-x86_64/egg/pybedtools creating build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/bigwig.py -> build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/__init__.py -> build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/venn_maker.py -> build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/plotting.py -> build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/contrib/bigbed.py -> build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/helpers.py -> build/bdist.linux-x86_64/egg/pybedtools creating build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_gzip_support.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_iter.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_cases.yaml -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_merge215.yaml -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/mpl-expected.png -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/gchart-expected.png -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_pathlib.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_contrib.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/__init__.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_merge227.yaml -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/tfuncs.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/regression_tests.py -> build/bdist.linux-x86_64/egg/pybedtools/test creating build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/a.igv_script -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/issue319.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/v.vcf -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/b.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/y.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/small.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/small.fastq -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/c.gff -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test.fa.fai -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/venn.c.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/issue_121.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.cram -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/bedpe.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/164.gtf -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/__init__.py -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/expand_test.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/a.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/d.gff -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.gff -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/x.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/exons.gff -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/x.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/hg19.gff -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/m1.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/venn.b.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/reads.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/genome.fa -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test.fa -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/a.links.html -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/egg/pybedtools/test/data copying build/lib.linux-x86_64-cpython-312/pybedtools/test/genomepy_integration.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_len_leak.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_helpers.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_1.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_issues.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_cbedtools.py -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-x86_64/egg/pybedtools/test copying build/lib.linux-x86_64-cpython-312/pybedtools/featurefuncs.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.pxd -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/bedtool.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/filenames.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/settings.py -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/featurefuncs.pyx -> build/bdist.linux-x86_64/egg/pybedtools copying build/lib.linux-x86_64-cpython-312/pybedtools/cbedtools.cpp -> build/bdist.linux-x86_64/egg/pybedtools byte-compiling build/bdist.linux-x86_64/egg/pybedtools/stats.py to stats.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/logger.py to logger.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/paths.py to paths.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/genome_registry.py to genome_registry.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/version.py to version.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/parallel.py to parallel.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/contrib/bigwig.py to bigwig.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/contrib/long_range_interaction.py to long_range_interaction.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/contrib/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/contrib/venn_maker.py to venn_maker.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/contrib/intersection_matrix.py to intersection_matrix.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/contrib/plotting.py to plotting.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/contrib/bigbed.py to bigbed.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/helpers.py to helpers.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_gzip_support.py to test_gzip_support.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_iter.py to test_iter.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_pathlib.py to test_pathlib.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_contrib.py to test_contrib.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/tfuncs.py to tfuncs.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/regression_tests.py to regression_tests.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/data/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/genomepy_integration.py to genomepy_integration.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_len_leak.py to test_len_leak.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_helpers.py to test_helpers.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_1.py to test_1.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_issues.py to test_issues.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/test/test_cbedtools.py to test_cbedtools.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/bedtool.py to bedtool.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/filenames.py to filenames.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/settings.py to settings.cpython-312.pyc creating stub loader for pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so creating stub loader for pybedtools/featurefuncs.cpython-312-x86_64-linux-gnu.so byte-compiling build/bdist.linux-x86_64/egg/pybedtools/cbedtools.py to cbedtools.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/featurefuncs.py to featurefuncs.cpython-312.pyc creating build/bdist.linux-x86_64/egg/EGG-INFO copying pybedtools.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO copying pybedtools.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pybedtools.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pybedtools.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO copying pybedtools.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO copying pybedtools.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt creating dist creating 'dist/pybedtools-0.10.0-py3.12-linux-x86_64.egg' and adding 'build/bdist.linux-x86_64/egg' to it removing 'build/bdist.linux-x86_64/egg' (and everything under it) Processing pybedtools-0.10.0-py3.12-linux-x86_64.egg creating /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/lib/python3.12/site-packages/pybedtools-0.10.0-py3.12-linux-x86_64.egg Extracting pybedtools-0.10.0-py3.12-linux-x86_64.egg to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/lib/python3.12/site-packages Adding pybedtools 0.10.0 to easy-install.pth file Installed /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/lib/python3.12/site-packages/pybedtools-0.10.0-py3.12-linux-x86_64.egg Processing dependencies for pybedtools==0.10.0 Searching for pysam==0.22.1 Best match: pysam 0.22.1 Adding pysam 0.22.1 to easy-install.pth file detected new path './pybedtools-0.10.0-py3.12-linux-x86_64.egg' Using /usr/lib/python3/dist-packages Searching for numpy==1.26.4 Best match: numpy 1.26.4 Adding numpy 1.26.4 to easy-install.pth file Installing f2py script to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/bin Installing f2py3 script to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/bin Installing f2py3.13 script to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/bin Installing f2py3.12 script to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/bin Using /usr/lib/python3/dist-packages Finished processing dependencies for pybedtools==0.10.0 I: pybuild base:311: cd /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build; python3.13 -m pytest -k "not test_chromsizes" ============================= test session starts ============================== platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build configfile: pyproject.toml plugins: typeguard-4.4.1 collected 511 items / 2 deselected / 509 selected pybedtools/test/test_1.py .............................................. [ 9%] .......................x..x.x...... [ 15%] pybedtools/test/test_cbedtools.py ...................................... [ 23%] . [ 23%] pybedtools/test/test_contrib.py .. [ 23%] pybedtools/test/test_gzip_support.py ........ [ 25%] pybedtools/test/test_helpers.py ...... [ 26%] pybedtools/test/test_issues.py ......................................... [ 34%] .. [ 35%] pybedtools/test/test_iter.py ........................................... [ 43%] ........................................................................ [ 57%] ........................................................................ [ 71%] ........................................................................ [ 86%] .................................................................... [ 99%] pybedtools/test/test_pathlib.py ... [100%] =========== 506 passed, 2 deselected, 3 xfailed in 201.09s (0:03:21) =========== I: pybuild pybuild:334: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; make clean doctest make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0/docs' rm -rf build/* source/autodocs/*.rst sphinx-build -b doctest -d build/doctrees source build/doctest Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, 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: /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.filenames.example_filename.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.filenames.list_example_files.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.chromsizes.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.chromsizes_to_file.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.cleanup.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.get_chromsizes_from_ucsc.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.get_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_bedtools_path.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst building [mo]: targets for 0 po files that are out of date writing output... building [doctest]: targets for 48 source files that are out of date updating environment: [new config] 157 added, 0 changed, 0 removed reading sources... [ 1%] 3-brief-examples reading sources... [ 1%] FAQs reading sources... [ 2%] autodoc_source /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/contrib/long_range_interaction.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.annotate reading sources... [ 5%] autodocs/pybedtools.bedtool.BedTool.any_hits reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.at reading sources... [ 7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bed6 reading sources... [ 9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.complement reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.count reading sources... [ 14%] autodocs/pybedtools.bedtool.BedTool.count_hits reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.coverage reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.cut reading sources... [ 16%] autodocs/pybedtools.bedtool.BedTool.each reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.expand reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.field_count reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.file_type reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.filter reading sources... [ 19%] autodocs/pybedtools.bedtool.BedTool.flank reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.genome_coverage reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.groupby reading sources... [ 21%] autodocs/pybedtools.bedtool.BedTool.head reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.igv reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.intersect reading sources... [ 23%] autodocs/pybedtools.bedtool.BedTool.introns reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.jaccard reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.liftover reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.links reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.map reading sources... [ 26%] autodocs/pybedtools.bedtool.BedTool.mask_fasta reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.merge reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.moveto reading sources... [ 28%] autodocs/pybedtools.bedtool.BedTool.multi_bam_coverage reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.multi_intersect reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.nucleotide_content reading sources... [ 30%] autodocs/pybedtools.bedtool.BedTool.overlap reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence reading sources... [ 33%] autodocs/pybedtools.bedtool.BedTool.random reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op reading sources... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection_bp reading sources... [ 37%] autodocs/pybedtools.bedtool.BedTool.randomstats reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.relative_distance reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.reldist reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.remove_invalid reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.save_seqs reading sources... [ 40%] autodocs/pybedtools.bedtool.BedTool.saveas reading sources... [ 41%] autodocs/pybedtools.bedtool.BedTool.seq reading sources... [ 41%] autodocs/pybedtools.bedtool.BedTool.sequence reading sources... [ 42%] autodocs/pybedtools.bedtool.BedTool.set_chromsizes reading sources... [ 43%] autodocs/pybedtools.bedtool.BedTool.shuffle reading sources... [ 43%] autodocs/pybedtools.bedtool.BedTool.slop reading sources... [ 44%] autodocs/pybedtools.bedtool.BedTool.sort reading sources... [ 45%] autodocs/pybedtools.bedtool.BedTool.split reading sources... [ 45%] autodocs/pybedtools.bedtool.BedTool.subtract reading sources... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix reading sources... [ 46%] autodocs/pybedtools.bedtool.BedTool.tabix_intervals reading sources... [ 47%] autodocs/pybedtools.bedtool.BedTool.tag_bam reading sources... [ 48%] autodocs/pybedtools.bedtool.BedTool.to_bam reading sources... [ 48%] autodocs/pybedtools.bedtool.BedTool.total_coverage reading sources... [ 49%] autodocs/pybedtools.bedtool.BedTool.truncate_to_chrom reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.union_bedgraphs reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.window reading sources... [ 51%] autodocs/pybedtools.bedtool.BedTool.window_maker reading sources... [ 52%] autodocs/pybedtools.bedtool.BedTool.with_attrs reading sources... [ 52%] autodocs/pybedtools.bedtool.example_bedtool reading sources... 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[ 59%] autodocs/pybedtools.contrib.long_range_interaction.tag_bedpe /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/contrib/long_range_interaction.py. self[section] = content reading sources... [ 59%] autodocs/pybedtools.contrib.plotting.BedToolsDemo reading sources... [ 60%] autodocs/pybedtools.contrib.plotting.ConfiguredBedToolsDemo reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.Track reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.TrackCollection reading sources... [ 62%] autodocs/pybedtools.contrib.plotting.binary_heatmap reading sources... [ 62%] autodocs/pybedtools.contrib.plotting.binary_summary reading sources... [ 63%] autodocs/pybedtools.contrib.venn_maker reading sources... [ 64%] autodocs/pybedtools.contrib.venn_maker.cleaned_intersect reading sources... [ 64%] autodocs/pybedtools.contrib.venn_maker.venn_maker reading sources... [ 65%] autodocs/pybedtools.debug_mode reading sources... [ 66%] autodocs/pybedtools.filenames.example_filename reading sources... [ 66%] autodocs/pybedtools.filenames.list_example_files reading sources... [ 67%] autodocs/pybedtools.helpers.chromsizes reading sources... [ 68%] autodocs/pybedtools.helpers.chromsizes_to_file reading sources... [ 68%] autodocs/pybedtools.helpers.cleanup reading sources... [ 69%] autodocs/pybedtools.helpers.get_chromsizes_from_ucsc reading sources... [ 69%] autodocs/pybedtools.helpers.get_tempdir reading sources... [ 70%] autodocs/pybedtools.helpers.set_bedtools_path reading sources... [ 71%] autodocs/pybedtools.helpers.set_tempdir reading sources... [ 71%] autodocs/pybedtools.parallel.parallel_apply reading sources... [ 72%] changes reading sources... [ 73%] create-a-bedtool-tutorial reading sources... [ 73%] default-arguments reading sources... [ 74%] each reading sources... [ 75%] filtering reading sources... [ 75%] flow-of-commands reading sources... [ 76%] history reading sources... [ 76%] includeme reading sources... [ 77%] index reading sources... [ 78%] intersections reading sources... [ 78%] intervals reading sources... [ 79%] intro reading sources... [ 80%] main reading sources... [ 80%] piping reading sources... [ 81%] pybedtools-dev-history reading sources... [ 82%] pybedtools.featurefuncs.TSS reading sources... [ 82%] pybedtools.featurefuncs.add_color reading sources... [ 83%] pybedtools.featurefuncs.bed2gff reading sources... [ 83%] pybedtools.featurefuncs.bedgraph_scale reading sources... [ 84%] pybedtools.featurefuncs.center reading sources... [ 85%] pybedtools.featurefuncs.extend_fields reading sources... [ 85%] pybedtools.featurefuncs.five_prime reading sources... [ 86%] pybedtools.featurefuncs.gff2bed reading sources... [ 87%] pybedtools.featurefuncs.greater_than reading sources... 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[100%] tutorial-contents WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. 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[autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.cis_trans_interactions' with 'contrib.long_range_interaction.cis_trans_interactions'. [autosummary.import_cycle] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy". [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.normalized_to_length /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename done preparing documents... done copying assets... copying assets: done running tests... Document: autodocs/pybedtools.bedtool.BedTool.annotate ------------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. 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Document: autodocs/pybedtools.bedtool.BedTool.total_coverage ------------------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.with_attrs -------------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.cbedtools.Interval ------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.cbedtools.create_interval_from_list ----------------------------------------------------------------- 1 items passed all tests: 1 tests in default 1 tests in 1 items. 1 passed and 0 failed. Test passed. Document: autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions ----------------------------------------------------------------------------------- 1 items passed all tests: 18 tests in default 18 tests in 1 items. 18 passed and 0 failed. Test passed. Document: autodocs/pybedtools.contrib.plotting.Track ---------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.filenames.list_example_files ---------------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.helpers.chromsizes ------------------------------------------------ 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.parallel.parallel_apply ----------------------------------------------------- 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: default-arguments --------------------------- 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: each -------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: filtering ------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: history ----------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: intersections ----------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: intervals ------------------- 1 items passed all tests: 50 tests in default 50 tests in 1 items. 50 passed and 0 failed. Test passed. Document: piping ---------------- 1 items passed all tests: 17 tests in default 17 tests in 1 items. 17 passed and 0 failed. Test passed. Document: save-results ---------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: topical-bam --------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-create-a-bedtool ---------------------------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-design-principles ----------------------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-genome ------------------------ 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: topical-iterators --------------------------- 1 items passed all tests: 20 tests in default 20 tests in 1 items. 20 passed and 0 failed. Test passed. Document: topical-low-level-ops ------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: topical-random ------------------------ 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-saving ------------------------ 1 items passed all tests: 14 tests in default 14 tests in 1 items. 14 passed and 0 failed. Test passed. Doctest summary =============== 387 tests 0 failures in tests 0 failures in setup code 0 failures in cleanup code build succeeded, 126 warnings. Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0/docs' I: pybuild pybuild:308: cp /build/reproducible-path/python-pybedtools-0.10.0/debian/mpl-expected.png /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/ ; python3 /build/reproducible-path/python-pybedtools-0.10.0/setup.py install --user ; export HOME=/build/reproducible-path/python-pybedtools-0.10.0/fakehome /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() error: can't combine user with prefix, exec_prefix/home, or install_(plat)base I: pybuild base:311: cd /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build; python3.12 -m pytest -k "not test_chromsizes" ============================= test session starts ============================== platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build configfile: pyproject.toml plugins: typeguard-4.4.1 collected 511 items / 2 deselected / 509 selected pybedtools/test/test_1.py .............................................. [ 9%] .......................x..x.x...... [ 15%] pybedtools/test/test_cbedtools.py ...................................... [ 23%] . [ 23%] pybedtools/test/test_contrib.py .. [ 23%] pybedtools/test/test_gzip_support.py ........ [ 25%] pybedtools/test/test_helpers.py ...... [ 26%] pybedtools/test/test_issues.py ......................................... [ 34%] .. [ 35%] pybedtools/test/test_iter.py ........................................... [ 43%] ........................................................................ [ 57%] ........................................................................ [ 71%] ........................................................................ [ 86%] .................................................................... [ 99%] pybedtools/test/test_pathlib.py ... [100%] =========== 506 passed, 2 deselected, 3 xfailed in 284.86s (0:04:44) =========== I: pybuild pybuild:334: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; make clean doctest make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0/docs' rm -rf build/* source/autodocs/*.rst sphinx-build -b doctest -d build/doctrees source build/doctest Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, 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: /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.filenames.example_filename.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.filenames.list_example_files.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.chromsizes.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.chromsizes_to_file.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.cleanup.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.get_chromsizes_from_ucsc.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.get_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_bedtools_path.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst building [mo]: targets for 0 po files that are out of date writing output... building [doctest]: targets for 48 source files that are out of date updating environment: [new config] 157 added, 0 changed, 0 removed reading sources... [ 1%] 3-brief-examples reading sources... [ 1%] FAQs reading sources... [ 2%] autodoc_source /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/contrib/long_range_interaction.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.annotate reading sources... [ 5%] autodocs/pybedtools.bedtool.BedTool.any_hits reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.at reading sources... [ 7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bed6 reading sources... [ 9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize reading sources... 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[ 30%] autodocs/pybedtools.bedtool.BedTool.overlap reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence reading sources... [ 33%] autodocs/pybedtools.bedtool.BedTool.random reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op reading sources... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection reading sources... 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[100%] tutorial-contents WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. 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[autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.cis_trans_interactions' with 'contrib.long_range_interaction.cis_trans_interactions'. [autosummary.import_cycle] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy". [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.normalized_to_length /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename done preparing documents... done copying assets... copying assets: done running tests... Document: autodocs/pybedtools.bedtool.BedTool.annotate ------------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.cat ------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.complement -------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.count --------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.coverage ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. 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Document: intervals ------------------- 1 items passed all tests: 50 tests in default 50 tests in 1 items. 50 passed and 0 failed. Test passed. Document: piping ---------------- 1 items passed all tests: 17 tests in default 17 tests in 1 items. 17 passed and 0 failed. Test passed. Document: save-results ---------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: topical-bam --------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-create-a-bedtool ---------------------------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-design-principles ----------------------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-genome ------------------------ 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: topical-iterators --------------------------- 1 items passed all tests: 20 tests in default 20 tests in 1 items. 20 passed and 0 failed. Test passed. Document: topical-low-level-ops ------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: topical-random ------------------------ 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-saving ------------------------ 1 items passed all tests: 14 tests in default 14 tests in 1 items. 14 passed and 0 failed. Test passed. Doctest summary =============== 387 tests 0 failures in tests 0 failures in setup code 0 failures in cleanup code build succeeded, 126 warnings. Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0/docs' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_installdirs -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3.13 setup.py install --root /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pybedtools/version.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_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:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/cbedtools.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/featurefuncs.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools running build_ext running install_lib creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/genome.txt -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/stats.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/featurefuncs.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/_Window.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/paths.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/filenames.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/settings.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/genome_registry.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/helpers.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/logger.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/stats.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/bedtool.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/version.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__pycache__ creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include/bedFile.h -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include/lineFileUtilities.h -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include/fileType.h -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include/gzstream.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include/bedFile.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include/gzstream.h -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include/fileType.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/cbedtools.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/logger.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/paths.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/cbedtools.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/genome_registry.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/version.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/parallel.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/featurefuncs.cpython-313-x86_64-linux-gnu.so -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/bigwig.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/__pycache__/bigwig.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/__pycache__/bigbed.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/__pycache__/long_range_interaction.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/__pycache__/venn_maker.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/__pycache__/intersection_matrix.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/long_range_interaction.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/venn_maker.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/intersection_matrix.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/plotting.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/bigbed.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_gzip_support.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_iter.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_1.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_helpers.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_cbedtools.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_issues.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/tfuncs.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_contrib.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_pathlib.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_gzip_support.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_iter.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__pycache__/test_len_leak.cpython-313-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_cases.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_merge215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/mpl-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/gchart-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_pathlib.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_contrib.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_merge227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_shuffle227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/prevent_open_file_regression -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/tfuncs.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/regression_tests.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.igv_script -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/1000genomes-example.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/issue319.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.50.200.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/hg38-problem.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/v.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/y.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/small.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.sorted.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/small.fastq -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/c.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.sorted.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/test.fa.fai -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/venn.c.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/issue_121.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/1000genomes-example.vcf.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.50.200.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.cram -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/vcf-stderr-test.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/tag_test1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/164.gtf -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/bedpe2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.1.100.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/vcf-stderr-test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/test_peaks.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/expand_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/mm9.bed12 -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/d.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/x.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/exons.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/test_bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/x.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.othersort.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/hg19.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/m1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/venn.b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/example.narrowPeak -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/tag_test2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed.gz.tbi -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/reads.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/genome.fa -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/issue319.vcf.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/gdc.1.100.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/test.fa -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/test_tsses.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.links.html -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/snps.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/hg38-base.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/a.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/issue319.out.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/multibamcov_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/democonfig.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/genomepy_integration.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_len_leak.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_1.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_issues.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_cbedtools.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/test_shuffle215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/cbedtools.pxd -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/bedtool.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/filenames.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/settings.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/featurefuncs.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/cbedtools.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/.pytest_cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/.pytest_cache/.gitignore -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/.pytest_cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/.pytest_cache/README.md -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/.pytest_cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/.pytest_cache creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/.pytest_cache/v creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/foo.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/stats.py to stats.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/logger.py to logger.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/paths.py to paths.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/genome_registry.py to genome_registry.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/version.py to version.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/parallel.py to parallel.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/bigwig.py to bigwig.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/long_range_interaction.py to long_range_interaction.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/venn_maker.py to venn_maker.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/intersection_matrix.py to intersection_matrix.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/plotting.py to plotting.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/contrib/bigbed.py to bigbed.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/helpers.py to helpers.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_gzip_support.py to test_gzip_support.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_iter.py to test_iter.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_pathlib.py to test_pathlib.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_contrib.py to test_contrib.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/tfuncs.py to tfuncs.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/regression_tests.py to regression_tests.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/data/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/genomepy_integration.py to genomepy_integration.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_len_leak.py to test_len_leak.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_helpers.py to test_helpers.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_1.py to test_1.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_issues.py to test_issues.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/test/test_cbedtools.py to test_cbedtools.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/bedtool.py to bedtool.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/filenames.py to filenames.cpython-313.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools/settings.py to settings.cpython-313.pyc running install_egg_info Copying pybedtools.egg-info to /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.13/dist-packages/pybedtools-0.10.0.egg-info Skipping SOURCES.txt running install_scripts I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py copying pybedtools/version.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_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:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/cbedtools.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/featurefuncs.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools running build_ext running install_lib creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/genome.txt -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/stats.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/featurefuncs.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/_Window.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/genome_registry.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/version.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/stats.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/helpers.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/logger.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/paths.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/settings.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/filenames.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__pycache__/bedtool.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__pycache__ creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include/bedFile.h -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include/lineFileUtilities.h -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include/fileType.h -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include/gzstream.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include/bedFile.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include/gzstream.h -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include/fileType.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/include copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/logger.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/paths.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/cbedtools.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/genome_registry.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/cbedtools.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/version.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/parallel.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/bigwig.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/__pycache__/bigwig.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/__pycache__/intersection_matrix.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/__pycache__/long_range_interaction.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/__pycache__/bigbed.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/__pycache__/venn_maker.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/long_range_interaction.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/venn_maker.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/intersection_matrix.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/plotting.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib/bigbed.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_gzip_support.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_iter.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_cbedtools.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_iter.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_len_leak.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/tfuncs.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/__init__.cpython-312.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_helpers.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_contrib.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_issues.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_gzip_support.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_1.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__pycache__/test_pathlib.cpython-312-pytest-8.3.4.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_cases.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_merge215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/mpl-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/gchart-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_pathlib.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_contrib.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_merge227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_shuffle227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/prevent_open_file_regression -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/tfuncs.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/regression_tests.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/a.igv_script -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/1000genomes-example.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/issue319.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.50.200.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/hg38-problem.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/v.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/y.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/small.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.sorted.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/small.fastq -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/c.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.sorted.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/test.fa.fai -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/venn.c.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/issue_121.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/1000genomes-example.vcf.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.50.200.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.cram -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/vcf-stderr-test.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/tag_test1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/164.gtf -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/bedpe2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.1.100.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/vcf-stderr-test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/test_peaks.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/expand_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/a.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/mm9.bed12 -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/d.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/x.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/exons.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/test_bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/x.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.othersort.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/hg19.gff -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/m1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/venn.b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/example.narrowPeak -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/tag_test2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/a.bed.gz.tbi -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/reads.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/genome.fa -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/issue319.vcf.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/gdc.1.100.bam -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/test.fa -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/test_tsses.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/a.links.html -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/snps.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/hg38-base.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/a.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/issue319.out.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/multibamcov_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/democonfig.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/genomepy_integration.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_len_leak.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_1.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_issues.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_cbedtools.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/test_shuffle215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/featurefuncs.cpython-312-x86_64-linux-gnu.so -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/cbedtools.pxd -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/bedtool.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/filenames.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/settings.py -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/featurefuncs.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/cbedtools.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/.pytest_cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/.pytest_cache/.gitignore -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/.pytest_cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/.pytest_cache/README.md -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/.pytest_cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/.pytest_cache/CACHEDIR.TAG -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/.pytest_cache creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/.pytest_cache/v creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/.pytest_cache/v/cache/stepwise -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/.pytest_cache/v/cache/nodeids -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/.pytest_cache/v/cache copying /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/foo.bed -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/stats.py to stats.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/logger.py to logger.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/paths.py to paths.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/genome_registry.py to genome_registry.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/version.py to version.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/parallel.py to parallel.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/bigwig.py to bigwig.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/long_range_interaction.py to long_range_interaction.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/venn_maker.py to venn_maker.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/intersection_matrix.py to intersection_matrix.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/plotting.py to plotting.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/contrib/bigbed.py to bigbed.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/helpers.py to helpers.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_gzip_support.py to test_gzip_support.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_iter.py to test_iter.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_pathlib.py to test_pathlib.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_contrib.py to test_contrib.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/tfuncs.py to tfuncs.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/regression_tests.py to regression_tests.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/data/__init__.py to __init__.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/genomepy_integration.py to genomepy_integration.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_len_leak.py to test_len_leak.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_helpers.py to test_helpers.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_1.py to test_1.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_issues.py to test_issues.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/test_cbedtools.py to test_cbedtools.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/bedtool.py to bedtool.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/filenames.py to filenames.cpython-312.pyc byte-compiling /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/settings.py to settings.cpython-312.pyc running install_egg_info Copying pybedtools.egg-info to /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools-0.10.0.egg-info Skipping SOURCES.txt running install_scripts debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0' 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 '/build/reproducible-path/python-pybedtools-0.10.0' dh_installdocs -O--buildsystem=pybuild dh_installdocs: warning: Cannot auto-detect main package for python-pybedtools-doc. If the default is wrong, please use --doc-main-package dh_sphinxdoc -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installexamples -O--buildsystem=pybuild dh_installexamples: warning: Cannot auto-detect main package for python-pybedtools-doc. If the default is wrong, please use --doc-main-package dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package pybedtools-bin: substitution variable ${python3:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-pybedtools-dbgsym' in '../python3-pybedtools-dbgsym_0.10.0-3_amd64.deb'. dpkg-deb: building package 'pybedtools-bin' in '../pybedtools-bin_0.10.0-3_all.deb'. dpkg-deb: building package 'python3-pybedtools' in '../python3-pybedtools_0.10.0-3_amd64.deb'. dpkg-deb: building package 'python-pybedtools-doc' in '../python-pybedtools-doc_0.10.0-3_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pybedtools_0.10.0-3_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pybedtools_0.10.0-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-source: info: using options from python-pybedtools-0.10.0/debian/source/options: --extend-diff-ignore=(pybedtools/version.py|docs/source/pybedtools.featurefuncs.*.rst) dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/737479 and its subdirectories I: Current time: Tue Dec 24 22:58:44 -12 2024 I: pbuilder-time-stamp: 1735124324 Wed Dec 25 10:58:47 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed Dec 25 10:58:47 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed Dec 25 11:04:04 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed Dec 25 11:04:05 UTC 2024 I: python-pybedtools_0.10.0-3_amd64.changes: Format: 1.8 Date: Tue, 24 Dec 2024 19:24:47 -0300 Source: python-pybedtools Binary: pybedtools-bin python-pybedtools-doc python3-pybedtools python3-pybedtools-dbgsym Architecture: all amd64 Version: 0.10.0-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Emmanuel Arias Description: pybedtools-bin - Scripts produced for pybedtools python-pybedtools-doc - Documentation for pybedtools library python3-pybedtools - Python 3 wrapper around BEDTools for bioinformatics work Closes: 1090283 Changes: python-pybedtools (0.10.0-3) unstable; urgency=medium . * Team Upload. * d/patches/fix-doctest-imports.py: Add patch from upstream to use explicit namespace in docstrings of long_range_interaction file (Closes: #1090283). Checksums-Sha1: 25b3ed2869d12c311b6a8091914d4f24710b5fc6 5300 pybedtools-bin_0.10.0-3_all.deb 039d6dc4e974de5ab5e60a9657bc9d088b8e8af2 274372 python-pybedtools-doc_0.10.0-3_all.deb 2b4da257b00bbbc3142a0ab29393bf3e1b3ffbfa 12293 python-pybedtools_0.10.0-3_amd64.buildinfo 7c7476ec19159e128679ac20986e0eaa82b34e50 2674240 python3-pybedtools-dbgsym_0.10.0-3_amd64.deb 4e9959300912bc4d04550c053dd030b116e88fef 12306716 python3-pybedtools_0.10.0-3_amd64.deb Checksums-Sha256: 2cadf1aba2cbf5cab21ff61f18b94e30bf5d1750a6043baf0261453e75b28d55 5300 pybedtools-bin_0.10.0-3_all.deb 44eeb2bfba51b0e15d67576272d2949a8a510177b477586895d2b65c9623e114 274372 python-pybedtools-doc_0.10.0-3_all.deb bdc579281152e325e4f13192d2f2db0cb77b2392120d4dec222a4a72fb9a1b1d 12293 python-pybedtools_0.10.0-3_amd64.buildinfo fe428a97541f86070dce132866438b12892cc7d319098f8fb56e2edf1aa533d0 2674240 python3-pybedtools-dbgsym_0.10.0-3_amd64.deb c51bb207f650c5cf2e62e1ff9991e2adc147d892f2ca5b526cf78a668c772ad9 12306716 python3-pybedtools_0.10.0-3_amd64.deb Files: 1da350195c73d0a61b72d5edae6de09f 5300 python optional pybedtools-bin_0.10.0-3_all.deb 8849eebf87337ae4cb63891f13d47798 274372 doc optional python-pybedtools-doc_0.10.0-3_all.deb 218d82fc5131461dfbd7a23e5cecd322 12293 python optional python-pybedtools_0.10.0-3_amd64.buildinfo 455d9e56d3d76654b016dd11216a400e 2674240 debug optional python3-pybedtools-dbgsym_0.10.0-3_amd64.deb 51b94bea0970f5a170e7a18b21e73316 12306716 python optional python3-pybedtools_0.10.0-3_amd64.deb Wed Dec 25 11:04:06 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_29-29313.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.56Cy3Wgr/python-pybedtools_0.10.0-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.56Cy3Wgr/python-pybedtools_0.10.0-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.56Cy3Wgr/python-pybedtools_0.10.0-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.56Cy3Wgr/b1/python-pybedtools_0.10.0-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.56Cy3Wgr/b2/python-pybedtools_0.10.0-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.496s) 0.496s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.149s) 0.149s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 828ms CPU time consumed: 821ms Wed Dec 25 11:04:08 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Wed Dec 25 11:04:08 UTC 2024 I: python-pybedtools from unstable built successfully and reproducibly on amd64. Wed Dec 25 11:04:09 UTC 2024 I: Submitting .buildinfo files to external archives: Wed Dec 25 11:04:09 UTC 2024 I: Submitting 16K b1/python-pybedtools_0.10.0-3_amd64.buildinfo.asc Wed Dec 25 11:04:11 UTC 2024 I: Submitting 16K b2/python-pybedtools_0.10.0-3_amd64.buildinfo.asc Wed Dec 25 11:04:12 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Dec 25 11:04:12 UTC 2024 I: Done submitting .buildinfo files. Wed Dec 25 11:04:12 UTC 2024 I: Removing signed python-pybedtools_0.10.0-3_amd64.buildinfo.asc files: removed './b1/python-pybedtools_0.10.0-3_amd64.buildinfo.asc' removed './b2/python-pybedtools_0.10.0-3_amd64.buildinfo.asc'