Thu Nov 21 08:30:05 UTC 2024 I: starting to build python-pybedtools/trixie/amd64 on jenkins on '2024-11-21 08:29' Thu Nov 21 08:30:05 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_28/39662/console.log Thu Nov 21 08:30:05 UTC 2024 I: Downloading source for trixie/python-pybedtools=0.10.0-2 --2024-11-21 08:30:05-- http://deb.debian.org/debian/pool/main/p/python-pybedtools/python-pybedtools_0.10.0-2.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_0.10.0-2.dsc’ 0K .. 100% 268M=0s 2024-11-21 08:30:05 (268 MB/s) - ‘python-pybedtools_0.10.0-2.dsc’ saved [2527/2527] Thu Nov 21 08:30:06 UTC 2024 I: python-pybedtools_0.10.0-2.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: 0.10.0-2 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 d9f0ba32f7e0101a470af632f782a1080cc90ba7 30512 python-pybedtools_0.10.0-2.debian.tar.xz Checksums-Sha256: 8b72ddd6dac632c3622848189f53787221b92c71a6f8ff0f802401135a3b6be7 12032584 python-pybedtools_0.10.0.orig.tar.xz 9f462ad75bb29f5e50ebea8ebc6b502325b4c0a505717dde98da12d04870a940 30512 python-pybedtools_0.10.0-2.debian.tar.xz Files: 602c5d35b956f4c3b5e736f13731d564 12032584 python-pybedtools_0.10.0.orig.tar.xz a3dbaa104357f070c979a8939b76c241 30512 python-pybedtools_0.10.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEE3lnVbvHK7ir4q61+p3sXeEcY/EFAmc3KWASHGVhbWFudUBk ZWJpYW4ub3JnAAoJEPqd7F3hHGPxy+gP/jJfxR19GQnHIlPtNlhB5knv/2uI4/YQ jZxDi0qbIaoksfFYbqcjlp68UV/gATTYquyQ5RprDmdwrFKTSXgb7AX0LoUF+2im rp+moIsip5ycACL1UfncSkQPzRcEQKtQGNUAkKhkEDKMVdYQ6fdZT/JWRObAxIVW 47wZsuruJtlhpfkVYFGf+TWMVig5SlG9r48VtQElqXB7gjq8Uog3QiKm/8Y8JB4U +jffq6yN0oC9sG2h6Fgyd5+hTMTELAImxYMfDq3hc6O3Sny0ruQ1d3R/R8KUmBKx FjulHIDKhJ+chcM7CrMx09xGBMUi+RS6qdmaFnBe3Dstm2koY9sv13dQdhCoNtT5 0vAG4H+j4S1TgNgZLQZJMsV4aU2yeH7Se4MteLtHT9Dd4/6GH+yXSI14gjWcfVYh IbTfe+dFZ/diEUyDJuozLs0zJ72Xr+eg+smZmf+0QRiGpd52Ec4dMLlbTH3CdYB3 N45ktFj7pRFusU66dM6eRIM6YMKsrfdaGJ8cvOWlUapmWArGEBei7np1qYSxBhCu ZvLJA0WF6fr7vbm7L6hoh5apVCaruAAcYFzRknRXHNxxu1yQxUClPy3m64Z2TcE1 tT239jZ4B5SX/5Rm+8mzIKBmZiptgctlX8sAw7A5Q/shrc7715buSntu7kUVYVqT hzRAua15hwid =4boL -----END PGP SIGNATURE----- Thu Nov 21 08:30:06 UTC 2024 I: Checking whether the package is not for us Thu Nov 21 08:30:06 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Thu Nov 21 08:30:06 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Thu Nov 21 08:38:38 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Dec 24 02:53:07 -12 2025 I: pbuilder-time-stamp: 1766587987 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_0.10.0-2.dsc] I: copying [./python-pybedtools_0.10.0.orig.tar.xz] I: copying [./python-pybedtools_0.10.0-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Nov 15 10:58:40 2024 gpgv: using RSA key 13796755BBC72BB8ABE2AEB5FA9DEC5DE11C63F1 gpgv: issuer "eamanu@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-pybedtools_0.10.0-2.dsc: no acceptable signature found 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_0.10.0-2.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2913717/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=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='73245b2e276b4147a4878c2252833874' 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='2913717' 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.LgPjKrJV/pbuilderrc_SXXs --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LgPjKrJV/b1 --logfile b1/build.log python-pybedtools_0.10.0-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2913717/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 ... 19969 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} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{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} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpng16-16t64{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} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{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} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-appdirs{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-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-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-six{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-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 libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx publicsuffix python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-numexpr python3-odf python3-olefile python3-openpyxl 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, 223 newly installed, 0 to remove and 0 not upgraded. Need to get 169 MB of archives. After unpacking 722 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024b-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1+b1 [23.2 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sgml-base all 1.31 [15.4 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-11 [91.5 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 bedtools amd64 2.31.1+dfsg-2 [678 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get: 64 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-1+b1 [3157 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 71 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20241024 [109 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.20+ds-2 [455 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get: 131 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get: 132 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 133 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 134 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 135 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 136 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 137 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get: 138 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get: 139 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get: 140 http://deb.debian.org/debian trixie/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 141 http://deb.debian.org/debian trixie/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 142 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.7-3 [2153 kB] Get: 143 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 144 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.7-3 [5124 kB] Get: 145 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 146 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.12.6-1 [1064 B] Get: 147 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 148 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get: 149 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 150 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 151 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 152 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 153 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 154 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 155 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 156 http://deb.debian.org/debian trixie/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 157 http://deb.debian.org/debian trixie/main amd64 libyaml-0-2 amd64 0.2.5-1+b2 [52.7 kB] Get: 158 http://deb.debian.org/debian trixie/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 159 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 160 http://deb.debian.org/debian trixie/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 161 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 162 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] Get: 163 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 164 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get: 165 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get: 166 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get: 167 http://deb.debian.org/debian trixie/main amd64 python3-babel all 2.16.0-1 [114 kB] Get: 168 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get: 169 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 170 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 171 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 172 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get: 173 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.0-2+b1 [264 kB] Get: 174 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get: 175 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 176 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get: 177 http://deb.debian.org/debian trixie/main amd64 python3-defusedxml all 0.7.1-2 [43.3 kB] Get: 178 http://deb.debian.org/debian trixie/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 179 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 180 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get: 181 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get: 182 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get: 183 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get: 184 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b5 [25.6 kB] Get: 185 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.13.1-6 [20.2 MB] Get: 186 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get: 187 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get: 188 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [32.9 kB] Get: 189 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get: 190 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.54.1-4+b1 [1631 kB] Get: 191 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 192 http://deb.debian.org/debian trixie/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 193 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 194 http://deb.debian.org/debian trixie/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 195 http://deb.debian.org/debian trixie/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 196 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB] Get: 197 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get: 198 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.7-3 [112 kB] Get: 199 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.0-2 [103 kB] Get: 200 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.7-1 [9444 B] Get: 201 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1+b1 [79.8 kB] Get: 202 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 203 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 204 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB] Get: 205 http://deb.debian.org/debian trixie/main amd64 sphinx-common all 7.4.7-4 [731 kB] Get: 206 http://deb.debian.org/debian trixie/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 207 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get: 208 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 209 http://deb.debian.org/debian trixie/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 210 http://deb.debian.org/debian trixie/main amd64 python3-sphinx all 7.4.7-4 [588 kB] Get: 211 http://deb.debian.org/debian trixie/main amd64 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 212 http://deb.debian.org/debian trixie/main amd64 python3-numpydoc all 1.6.0-2 [49.6 kB] Get: 213 http://deb.debian.org/debian trixie/main amd64 python3-pandas-lib amd64 2.2.3+dfsg-5+b1 [7307 kB] Get: 214 http://deb.debian.org/debian trixie/main amd64 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 215 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 216 http://deb.debian.org/debian trixie/main amd64 python3-psutil amd64 5.9.8-2 [225 kB] Get: 217 http://deb.debian.org/debian trixie/main amd64 python3-pysam amd64 0.22.1+ds-2+b2 [4412 kB] Get: 218 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 219 http://deb.debian.org/debian trixie/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] Get: 220 http://deb.debian.org/debian trixie/main amd64 zip amd64 3.0-14 [233 kB] Get: 221 http://deb.debian.org/debian trixie/main amd64 unzip amd64 6.0-28 [166 kB] Get: 222 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 223 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.4.2-1 [28.3 MB] Fetched 169 MB in 19s (8658 kB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19969 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. 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Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024b-3_all.deb ... Unpacking tzdata (2024b-3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1+b1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... 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 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21351 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sgml-base. 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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_0.10.0-2_source.changes dpkg-buildpackage: info: source package python-pybedtools dpkg-buildpackage: info: source version 0.10.0-2 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: python3.12 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 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/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/logger.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/parallel.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/settings.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/stats.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/bedtool.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/tfuncs.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/test_len_leak.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 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_gzip_support.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/regression_tests.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_pathlib.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/genomepy_integration.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 creating /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/bigbed.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/bigwig.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/plotting.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 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 creating pybedtools.egg-info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt writing manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'pybedtools' warning: no previously-included files matching '__pycache__' found under directory '*' warning: no previously-included files matching '*.py[co]' found under directory '*' adding license file 'LICENSE.txt' writing manifest file 'pybedtools.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/_Window.pyx -> /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/test_tsses.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/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/hg38-base.bed -> /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/test.fa -> /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/m1.bed -> /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/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/multibamcov_test.bed -> /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/snps.bed.gz -> /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/example.narrowPeak -> /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/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/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/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/164.gtf -> /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/small.fastq -> /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/mm9.bed12 -> /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/exons.gff -> /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/gdc.cram -> /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/issue319.out.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/small.bam -> /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.othersort.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/issue_121.bam -> /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/venn.b.bed -> /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/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/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/bedpe2.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/1000genomes-example.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/test_bedpe.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/test_peaks.bed -> /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/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/expand_test.bed -> /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/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/issue319.bed -> /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/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/a.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/data/democonfig.yaml -> /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/x.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/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/tag_test1.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/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/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/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 creating build/temp.linux-x86_64-cpython-312 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 v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst [autosummary] generating autosummary for: /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:455: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. warn(msg) /usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: 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. warn(msg) reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool /usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. warn(msg) reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits reading sources... 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[ 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... [ 87%] pybedtools.featurefuncs.less_than reading sources... [ 88%] pybedtools.featurefuncs.midpoint reading sources... [ 89%] pybedtools.featurefuncs.normalized_to_length reading sources... [ 89%] pybedtools.featurefuncs.rename reading sources... [ 90%] pybedtools.featurefuncs.three_prime reading sources... [ 90%] save-results reading sources... [ 91%] scripts reading sources... [ 92%] sh-comparison reading sources... [ 92%] topical-bam reading sources... [ 93%] topical-bam-semantics reading sources... [ 94%] topical-comparisons reading sources... [ 94%] topical-create-a-bedtool reading sources... [ 95%] topical-design-principles reading sources... [ 96%] topical-documentation-contents reading sources... [ 96%] topical-genome reading sources... [ 97%] topical-iterators reading sources... [ 97%] topical-low-level-ops reading sources... [ 98%] topical-random reading sources... [ 99%] topical-saving reading sources... [ 99%] topical-wrapping reading sources... [100%] tutorial-contents WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.links' with 'bedtool.BedTool.links'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.igv' with 'bedtool.BedTool.igv'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window_maker' with 'bedtool.BedTool.window_maker'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.groupby' with 'bedtool.BedTool.groupby'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.expand' with 'bedtool.BedTool.expand'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.each' with 'bedtool.BedTool.each'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.filter' with 'bedtool.BedTool.filter'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.split' with 'bedtool.BedTool.split'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.truncate_to_chrom' with 'bedtool.BedTool.truncate_to_chrom'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.remove_invalid' with 'bedtool.BedTool.remove_invalid'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.three_prime' with 'featurefuncs.three_prime'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.five_prime' with 'featurefuncs.five_prime'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.TSS' with 'featurefuncs.TSS'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.extend_fields' with 'featurefuncs.extend_fields'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.center' with 'featurefuncs.center'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.midpoint' with 'featurefuncs.midpoint'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.greater_than' with 'featurefuncs.greater_than'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.less_than' with 'featurefuncs.less_than'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bedgraph_scale' with 'featurefuncs.bedgraph_scale'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.add_color' with 'featurefuncs.add_color'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.gff2bed' with 'featurefuncs.gff2bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bed2gff' with 'featurefuncs.bed2gff'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.all_hits' with 'bedtool.BedTool.all_hits'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.any_hits' with 'bedtool.BedTool.any_hits'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count_hits' with 'bedtool.BedTool.count_hits'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix_intervals' with 'bedtool.BedTool.tabix_intervals'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix' with 'bedtool.BedTool.tabix'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bgzip' with 'bedtool.BedTool.bgzip'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.head' with 'bedtool.BedTool.head'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count' with 'bedtool.BedTool.count'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.field_count' with 'bedtool.BedTool.field_count'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.file_type' with 'bedtool.BedTool.file_type'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.parallel_apply' with 'bedtool.BedTool.parallel_apply'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomstats' with 'bedtool.BedTool.randomstats'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection' with 'bedtool.BedTool.randomintersection'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection_bp' with 'bedtool.BedTool.randomintersection_bp'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_subset' with 'bedtool.BedTool.random_subset'. 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[ 91%] scripts writing output... [ 92%] sh-comparison writing output... [ 92%] topical-bam writing output... [ 93%] topical-bam-semantics writing output... [ 94%] topical-comparisons writing output... [ 94%] topical-create-a-bedtool writing output... [ 95%] topical-design-principles writing output... [ 96%] topical-documentation-contents writing output... [ 96%] topical-genome writing output... [ 97%] topical-iterators writing output... [ 97%] topical-low-level-ops writing output... [ 98%] topical-random writing output... [ 99%] topical-saving writing output... [ 99%] topical-wrapping writing output... [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. /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. /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. /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: '$'. Retrying in relaxed mode. /build/reproducible-path/python-pybedtools-0.10.0/docs/source/default-arguments.rst:35: WARNING: Lexing literal_block '$ intersectBed -a a.bed -b b.bed -u > tmpfile' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-design-principles.rst:120: WARNING: unknown option: 'mergeBed -i' /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-design-principles.rst:127: WARNING: unknown option: '-i' 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... [ 46%] pybedtools.contrib.intersection_matrix highlighting module code... [ 54%] pybedtools.contrib.long_range_interaction highlighting module code... [ 62%] pybedtools.contrib.plotting highlighting module code... [ 69%] pybedtools.contrib.venn_maker highlighting module code... [ 77%] pybedtools.featurefuncs highlighting module code... [ 85%] pybedtools.filenames highlighting module code... [ 92%] pybedtools.helpers highlighting module code... [100%] pybedtools.parallel writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 133 warnings. The HTML pages are in docs/html. make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0' dh_auto_test -O--buildsystem=pybuild I: pybuild pybuild:308: cp /build/reproducible-path/python-pybedtools-0.10.0/debian/mpl-expected.png /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/ ; 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 creating 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/logger.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/parallel.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/helpers.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/paths.py -> build/lib.linux-x86_64-cpython-312/pybedtools copying pybedtools/bedtool.py -> build/lib.linux-x86_64-cpython-312/pybedtools creating build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/tfuncs.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/test_len_leak.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_1.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_pathlib.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test copying pybedtools/test/test_issues.py -> build/lib.linux-x86_64-cpython-312/pybedtools/test creating build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-cpython-312/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> 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/venn_maker.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/__init__.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:218: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/_Window.pyx -> build/lib.linux-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/test_tsses.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/gdc.1.100.bam -> 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/hg38-problem.bed -> 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/gdc.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/bedpe.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/example.narrowPeak -> 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/vcf-stderr-test.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/vcf-stderr-test.vcf -> 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/rmsk.hg18.chr21.small.bed -> 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/gdc.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/gdc.bam -> 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/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> 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/a.links.html -> 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/venn.c.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/genome.fa -> 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/c.gff -> 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/reads.bam -> 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/rmsk.hg18.chr21.small.bed.gz -> 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/x.bam -> 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/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/test_bedpe.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/test_peaks.bed -> 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/BEAF_Kc_Bushey_2009.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/issue319.vcf.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue319.bed -> 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/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.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/d.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/v.vcf -> 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/tag_test1.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/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-cpython-312/pybedtools/test/data copying pybedtools/test/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 creating build/bdist.linux-x86_64/egg creating 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/genome_registry.py -> 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/logger.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 creating 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/lineFileUtilities.h -> 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/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.h -> build/bdist.linux-x86_64/egg/pybedtools/include 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 creating 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/test_contrib.py -> 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/test_merge215.yaml -> 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/gchart-expected.png -> 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_cbedtools.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/test_tsses.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/gdc.1.100.bam -> 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/hg38-problem.bed -> 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/gdc.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/bedpe.bed -> 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/multibamcov_test.bed -> 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/snps.bed.gz -> 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/example.narrowPeak -> 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/vcf-stderr-test.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/vcf-stderr-test.vcf -> 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/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/small.fastq -> 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/mm9.bed12 -> 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/exons.gff -> 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/gdc.cram -> 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/issue319.out.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/small.bam -> 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.othersort.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/issue_121.bam -> 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/venn.b.bed -> 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/reads.bam -> 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/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/bedpe2.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/1000genomes-example.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/test_bedpe.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/test_peaks.bed -> 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/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/expand_test.bed -> 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/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/issue319.bed -> 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/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/a.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/data/democonfig.yaml -> 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/x.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/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/tag_test1.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/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/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/test_iter.py -> 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/mpl-expected.png -> 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/__init__.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/test/regression_tests.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_pathlib.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_cases.yaml -> build/bdist.linux-x86_64/egg/pybedtools/test 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_issues.py -> build/bdist.linux-x86_64/egg/pybedtools/test 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/featurefuncs.cpython-312-x86_64-linux-gnu.so -> 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/parallel.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/__init__.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/helpers.py -> 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 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/paths.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/intersection_matrix.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/contrib/long_range_interaction.py -> 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/venn_maker.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/__init__.py -> build/bdist.linux-x86_64/egg/pybedtools/contrib copying build/lib.linux-x86_64-cpython-312/pybedtools/bedtool.py -> build/bdist.linux-x86_64/egg/pybedtools 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/logger.py to logger.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/test_contrib.py to test_contrib.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_cbedtools.py to test_cbedtools.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/test_iter.py to test_iter.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/__init__.py to __init__.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/test_1.py to test_1.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_helpers.py to test_helpers.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_issues.py to test_issues.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/parallel.py to parallel.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/settings.py to settings.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/stats.py to stats.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/contrib/intersection_matrix.py to intersection_matrix.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/contrib/long_range_interaction.py to long_range_interaction.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/venn_maker.py to venn_maker.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/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-x86_64/egg/pybedtools/bedtool.py to bedtool.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_3.12_pybedtools/build; python3.12 -m pytest -k "not test_chromsizes" ============================= test session starts ============================== platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 rootdir: /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 19.73s ================= 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 v7.4.7 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst [autosummary] generating autosummary for: /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:455: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. warn(msg) /usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: 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. warn(msg) reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool /usr/lib/python3/dist-packages/numpydoc/docscrape.py:455: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. warn(msg) 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... 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Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.links' with 'bedtool.BedTool.links'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.igv' with 'bedtool.BedTool.igv'. 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Replace 'pybedtools.bedtool.BedTool.truncate_to_chrom' with 'bedtool.BedTool.truncate_to_chrom'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.remove_invalid' with 'bedtool.BedTool.remove_invalid'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.three_prime' with 'featurefuncs.three_prime'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.five_prime' with 'featurefuncs.five_prime'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.TSS' with 'featurefuncs.TSS'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.extend_fields' with 'featurefuncs.extend_fields'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.center' with 'featurefuncs.center'. 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Replace 'pybedtools.bedtool.BedTool.count_hits' with 'bedtool.BedTool.count_hits'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix_intervals' with 'bedtool.BedTool.tabix_intervals'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix' with 'bedtool.BedTool.tabix'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bgzip' with 'bedtool.BedTool.bgzip'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.head' with 'bedtool.BedTool.head'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count' with 'bedtool.BedTool.count'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.field_count' with 'bedtool.BedTool.field_count'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.file_type' with 'bedtool.BedTool.file_type'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.parallel_apply' with 'bedtool.BedTool.parallel_apply'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomstats' with 'bedtool.BedTool.randomstats'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection' with 'bedtool.BedTool.randomintersection'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection_bp' with 'bedtool.BedTool.randomintersection_bp'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_subset' with 'bedtool.BedTool.random_subset'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_jaccard' with 'bedtool.BedTool.random_jaccard'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_op' with 'bedtool.BedTool.random_op'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.saveas' with 'bedtool.BedTool.saveas'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.moveto' with 'bedtool.BedTool.moveto'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cat' with 'bedtool.BedTool.cat'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.at' with 'bedtool.BedTool.at'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.absolute_distance' with 'bedtool.BedTool.absolute_distance'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cut' with 'bedtool.BedTool.cut'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.total_coverage' with 'bedtool.BedTool.total_coverage'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.with_attrs' with 'bedtool.BedTool.with_attrs'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.as_intervalfile' with 'bedtool.BedTool.as_intervalfile'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.introns' with 'bedtool.BedTool.introns'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.set_chromsizes' with 'bedtool.BedTool.set_chromsizes'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.print_sequence' with 'bedtool.BedTool.print_sequence'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.save_seqs' with 'bedtool.BedTool.save_seqs'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.seq' with 'bedtool.BedTool.seq'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.liftover' with 'bedtool.BedTool.liftover'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.colormap_normalize' with 'bedtool.BedTool.colormap_normalize'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.relative_distance' with 'bedtool.BedTool.relative_distance'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.example_bedtool' with 'bedtool.example_bedtool'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.list_example_files' with 'filenames.list_example_files'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.example_filename' with 'filenames.example_filename'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.Interval' with 'cbedtools.Interval'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.create_interval_from_list' with 'cbedtools.create_interval_from_list'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_bedtools_path' with 'helpers.set_bedtools_path'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_tempdir' with 'helpers.get_tempdir'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_tempdir' with 'helpers.set_tempdir'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.cleanup' with 'helpers.cleanup'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.debug_mode' with 'debug_mode'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_chromsizes_from_ucsc' with 'helpers.get_chromsizes_from_ucsc'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes' with 'helpers.chromsizes'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes_to_file' with 'helpers.chromsizes_to_file'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.parallel.parallel_apply' with 'parallel.parallel_apply'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.Track' with 'contrib.plotting.Track'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.TrackCollection' with 'contrib.plotting.TrackCollection'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_heatmap' with 'contrib.plotting.binary_heatmap'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_summary' with 'contrib.plotting.binary_summary'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.BedToolsDemo' with 'contrib.plotting.BedToolsDemo'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.ConfiguredBedToolsDemo' with 'contrib.plotting.ConfiguredBedToolsDemo'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bam_to_bigwig' with 'contrib.bigwig.bam_to_bigwig'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bedgraph_to_bigwig' with 'contrib.bigwig.bedgraph_to_bigwig'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.wig_to_bigwig' with 'contrib.bigwig.wig_to_bigwig'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed' with 'contrib.bigbed.bigbed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed_to_bed' with 'contrib.bigbed.bigbed_to_bed'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.IntersectionMatrix' with 'contrib.IntersectionMatrix'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker' with 'contrib.venn_maker'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.venn_maker' with 'contrib.venn_maker.venn_maker'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. 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'. /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy". 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 running tests... Document: intervals ------------------- 1 items passed all tests: 50 tests in default 50 tests in 1 items. 50 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: 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: 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-saving ------------------------ 1 items passed all tests: 14 tests in default 14 tests in 1 items. 14 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-genome ------------------------ 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 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-iterators --------------------------- 1 items passed all tests: 20 tests in default 20 tests in 1 items. 20 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: intersections ----------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 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: history ----------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 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: piping ---------------- 1 items passed all tests: 17 tests in default 17 tests in 1 items. 17 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. Doctest summary =============== 223 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 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:218: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/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 creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib creating /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12 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/.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/.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/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 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/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/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/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/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/featurefuncs.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/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__/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__/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__/bedtool.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__/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__/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__/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__/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__/logger.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.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/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/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/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.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/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/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/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/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/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/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/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_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_cbedtools.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_pathlib.cpython-312-pytest-8.3.3.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-8.3.3.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_cbedtools.cpython-312-pytest-8.3.3.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_len_leak.cpython-312-pytest-8.3.3.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__/test_1.cpython-312-pytest-8.3.3.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-8.3.3.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-8.3.3.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-8.3.3.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-8.3.3.pyc -> /build/reproducible-path/python-pybedtools-0.10.0/debian/python3-pybedtools/usr/lib/python3.12/dist-packages/pybedtools/test/__pycache__ 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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.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/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/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/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/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/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/__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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/test_iter.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/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/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/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/__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_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/test/regression_tests.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_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_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_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/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_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/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/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/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/parallel.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/__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/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/helpers.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/_Window.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/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/paths.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/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/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/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/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__/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/__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__/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__/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/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/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/__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/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/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/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/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/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/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/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_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/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/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_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/__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/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/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_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_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/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_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/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/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/__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/settings.py to settings.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/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/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/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/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/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/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/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/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/__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/bedtool.py to bedtool.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 'pybedtools-bin' in '../pybedtools-bin_0.10.0-2_all.deb'. dpkg-deb: building package 'python3-pybedtools' in '../python3-pybedtools_0.10.0-2_amd64.deb'. dpkg-deb: building package 'python3-pybedtools-dbgsym' in '../python3-pybedtools-dbgsym_0.10.0-2_amd64.deb'. dpkg-deb: building package 'python-pybedtools-doc' in '../python-pybedtools-doc_0.10.0-2_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pybedtools_0.10.0-2_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pybedtools_0.10.0-2_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/2913717 and its subdirectories I: Current time: Wed Dec 24 03:01:36 -12 2025 I: pbuilder-time-stamp: 1766588496 Thu Nov 21 08:38:38 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Thu Nov 21 08:38:38 UTC 2024 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Thu Nov 21 08:50:59 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Thu Nov 21 08:50:59 UTC 2024 I: python-pybedtools_0.10.0-2_amd64.changes: Format: 1.8 Date: Thu, 14 Nov 2024 22:58:17 -0300 Source: python-pybedtools Binary: pybedtools-bin python-pybedtools-doc python3-pybedtools python3-pybedtools-dbgsym Architecture: all amd64 Version: 0.10.0-2 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: 1081673 Changes: python-pybedtools (0.10.0-2) unstable; urgency=medium . * Team upload. * d/patches/416.patch: Apply patch from upstream to fix Python3.13 issues in build (Closes: #1081673). Checksums-Sha1: 0bf929e41e76be74558a47e9d0fa36742ad5a743 5208 pybedtools-bin_0.10.0-2_all.deb dbf55b7b71aa1eefde6be20a7a0c50405f5c9c8f 274324 python-pybedtools-doc_0.10.0-2_all.deb 430e14abb17e184b3aec8abd72e9274e5266d751 11987 python-pybedtools_0.10.0-2_amd64.buildinfo 9f5a8a91413daac7a46f5cc4d0b9bb5996b3491f 1415808 python3-pybedtools-dbgsym_0.10.0-2_amd64.deb 05301f950aafb8e6bafcb07c25ee6d63a9394536 12227432 python3-pybedtools_0.10.0-2_amd64.deb Checksums-Sha256: 4265ab62a4cbfe83c3e5b22621ed57a377fc6934d884259d37278b84e361f92d 5208 pybedtools-bin_0.10.0-2_all.deb 999e5868341d670ab384964e50a99e920964ea74eaa3dd767804b1532caeb14f 274324 python-pybedtools-doc_0.10.0-2_all.deb 2c3b91ad7d69f3760dfa063542175fbed6df0b2b2c3d2b33ee1a8f8089092b69 11987 python-pybedtools_0.10.0-2_amd64.buildinfo bd0545d59ec5b84044987010e411be4f1eb9e229d26333d1df5218392c645104 1415808 python3-pybedtools-dbgsym_0.10.0-2_amd64.deb 6f89006c44484f080eadd592ec8d904684dbc7770d2f77b8d54399e9aee109ba 12227432 python3-pybedtools_0.10.0-2_amd64.deb Files: 16916716bf5b70b83d53d549eb5143a4 5208 python optional pybedtools-bin_0.10.0-2_all.deb 7754df6bd7de9e85bc0f5a34d76c2c03 274324 doc optional python-pybedtools-doc_0.10.0-2_all.deb 95b2001820c372d3756de2ea6c7a97b3 11987 python optional python-pybedtools_0.10.0-2_amd64.buildinfo cc6a6f9e74ee239e2d981c53b4c0a51f 1415808 debug optional python3-pybedtools-dbgsym_0.10.0-2_amd64.deb 8fd167375c7ee9c40e3a05eaa500662f 12227432 python optional python3-pybedtools_0.10.0-2_amd64.deb Thu Nov 21 08:51:00 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_28-39662.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.LgPjKrJV/python-pybedtools_0.10.0-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.LgPjKrJV/python-pybedtools_0.10.0-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.LgPjKrJV/python-pybedtools_0.10.0-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.LgPjKrJV/b1/python-pybedtools_0.10.0-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.LgPjKrJV/b2/python-pybedtools_0.10.0-2_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: 0.547s) 0.547s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.175s) 0.175s 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: 881ms CPU time consumed: 882ms Thu Nov 21 08:51:02 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Thu Nov 21 08:51:02 UTC 2024 I: python-pybedtools from trixie built successfully and reproducibly on amd64. Thu Nov 21 08:51:03 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Nov 21 08:51:03 UTC 2024 I: Submitting 16K b1/python-pybedtools_0.10.0-2_amd64.buildinfo.asc Thu Nov 21 08:51:05 UTC 2024 I: Submitting 16K b2/python-pybedtools_0.10.0-2_amd64.buildinfo.asc Thu Nov 21 08:51:06 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Nov 21 08:51:06 UTC 2024 I: Done submitting .buildinfo files. Thu Nov 21 08:51:06 UTC 2024 I: Removing signed python-pybedtools_0.10.0-2_amd64.buildinfo.asc files: removed './b1/python-pybedtools_0.10.0-2_amd64.buildinfo.asc' removed './b2/python-pybedtools_0.10.0-2_amd64.buildinfo.asc'