Thu Dec 19 02:54:49 UTC 2024 I: starting to build python-pybedtools/unstable/i386 on jenkins on '2024-12-19 02:54' Thu Dec 19 02:54:49 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_8/53476/console.log Thu Dec 19 02:54:49 UTC 2024 I: Downloading source for unstable/python-pybedtools=0.10.0-2 --2024-12-19 02:54:49-- 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% 335M=0s 2024-12-19 02:54:49 (335 MB/s) - ‘python-pybedtools_0.10.0-2.dsc’ saved [2527/2527] Thu Dec 19 02:54:49 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 Dec 19 02:54:49 UTC 2024 I: Checking whether the package is not for us Thu Dec 19 02:54:49 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Thu Dec 19 02:54:49 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Thu Dec 19 03:00:12 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jan 20 21:17:50 -12 2026 I: pbuilder-time-stamp: 1768987070 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job 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/28056/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='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='a30baf4ed6504eacac99e8e1f74ae1e3' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='28056' 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.IEtPazQ2/pbuilderrc_q9ua --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.IEtPazQ2/b1 --logfile b1/build.log python-pybedtools_0.10.0-2.dsc' SUDO_GID='112' SUDO_UID='107' 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 ionos16-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/28056/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: i386 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 ... 19953 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} libproc2-0{a} libpsl5t64{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-r8.0{a} libraqm0{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1t64{a} 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} procps{a} python-babel-localedata{a} python-matplotlib-data{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-attr{a} python3-autocommand{a} python3-babel{a} python3-brotli{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-fonttools{a} python3-fs{a} python3-idna{a} python3-imagesize{a} python3-inflect{a} python3-iniconfig{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-kiwisolver{a} python3-lxml{a} python3-lz4{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-more-itertools{a} python3-mpmath{a} python3-numpy{a} python3-numpydoc{a} python3-packaging{a} python3-pandas{a} python3-pandas-lib{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-platformdirs{a} python3-pluggy{a} python3-psutil{a} python3-pygments{a} python3-pyparsing{a} python3-pysam{a} python3-pytest{a} python3-requests{a} python3-roman{a} python3-scipy{a} python3-setuptools{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sympy{a} python3-tabulate{a} python3-tk{a} python3-typeguard{a} python3-typing-extensions{a} python3-tz{a} python3-ufolib2{a} python3-urllib3{a} python3-yaml{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-tk{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} python3.13-tk{a} r-base-core{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} tk8.6-blt2.5{a} tzdata{a} ucf{a} unicode-data{a} unzip{a} x11-common{a} xdg-utils{a} xml-core{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl isympy-common javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix python3-bottleneck python3-bs4 python3-cssselect python3-html5lib python3-numexpr python3-odf python3-olefile python3-openpyxl python3-pooch python3-tables r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 232 newly installed, 0 to remove and 0 not upgraded. Need to get 183 MB of archives. After unpacking 780 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.8-3 [816 kB] Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 3 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.8-3 [2239 kB] Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.7-1 [26.8 kB] Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024b-4 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 9 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB] Get: 10 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 11 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 12 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 13 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 14 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB] Get: 16 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB] Get: 17 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB] Get: 18 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB] Get: 19 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.8-3 [1968 kB] Get: 20 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.8-3 [677 kB] Get: 21 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.7-1 [9712 B] Get: 22 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.7-1 [27.8 kB] Get: 23 http://deb.debian.org/debian unstable/main i386 libpython3.13-minimal i386 3.13.1-2 [858 kB] Get: 24 http://deb.debian.org/debian unstable/main i386 python3.13-minimal i386 3.13.1-2 [2260 kB] Get: 25 http://deb.debian.org/debian unstable/main i386 sgml-base all 1.31 [15.4 kB] Get: 26 http://deb.debian.org/debian unstable/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 27 http://deb.debian.org/debian unstable/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 28 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 29 http://deb.debian.org/debian unstable/main i386 openssl i386 3.3.2-2 [1387 kB] Get: 30 http://deb.debian.org/debian unstable/main i386 ca-certificates all 20240203 [158 kB] Get: 31 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 32 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 33 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 34 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-3 [201 kB] Get: 35 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 36 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB] Get: 37 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB] Get: 38 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 39 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 40 http://deb.debian.org/debian unstable/main i386 ucf all 3.0045 [45.2 kB] Get: 41 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB] Get: 42 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB] Get: 43 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 44 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 45 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-3 [723 kB] Get: 46 http://deb.debian.org/debian unstable/main i386 bedtools i386 2.31.1+dfsg-2 [745 kB] Get: 47 http://deb.debian.org/debian unstable/main i386 libtcl8.6 i386 8.6.15+dfsg-2 [1103 kB] Get: 48 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 49 http://deb.debian.org/debian unstable/main i386 libpng16-16t64 i386 1.6.44-3 [288 kB] Get: 50 http://deb.debian.org/debian unstable/main i386 libfreetype6 i386 2.13.3+dfsg-1 [464 kB] Get: 51 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 52 http://deb.debian.org/debian unstable/main i386 fonts-dejavu-core all 2.37-8 [840 kB] Get: 53 http://deb.debian.org/debian unstable/main i386 fontconfig-config i386 2.15.0-1.1+b1 [318 kB] Get: 54 http://deb.debian.org/debian unstable/main i386 libfontconfig1 i386 2.15.0-1.1+b1 [402 kB] Get: 55 http://deb.debian.org/debian unstable/main i386 libxau6 i386 1:1.0.11-1 [20.7 kB] Get: 56 http://deb.debian.org/debian unstable/main i386 libxdmcp6 i386 1:1.1.5-1 [28.2 kB] Get: 57 http://deb.debian.org/debian unstable/main i386 libxcb1 i386 1.17.0-2+b1 [148 kB] Get: 58 http://deb.debian.org/debian unstable/main i386 libx11-data all 2:1.8.10-2 [337 kB] Get: 59 http://deb.debian.org/debian unstable/main i386 libx11-6 i386 2:1.8.10-2 [834 kB] Get: 60 http://deb.debian.org/debian unstable/main i386 libxrender1 i386 1:0.9.10-1.1+b3 [28.8 kB] Get: 61 http://deb.debian.org/debian unstable/main i386 libxft2 i386 2.3.6-1+b3 [55.3 kB] Get: 62 http://deb.debian.org/debian unstable/main i386 libxext6 i386 2:1.3.4-1+b2 [52.6 kB] Get: 63 http://deb.debian.org/debian unstable/main i386 x11-common all 1:7.7+23.1 [216 kB] Get: 64 http://deb.debian.org/debian unstable/main i386 libxss1 i386 1:1.2.3-1+b2 [17.3 kB] Get: 65 http://deb.debian.org/debian unstable/main i386 libtk8.6 i386 8.6.15-1 [833 kB] Get: 66 http://deb.debian.org/debian unstable/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-7 [616 kB] Get: 67 http://deb.debian.org/debian unstable/main i386 blt i386 2.5.3+dfsg-7 [6024 B] Get: 68 http://deb.debian.org/debian unstable/main i386 cython3 i386 3.0.11+dfsg-1+b1 [3019 kB] Get: 69 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.22 [90.5 kB] Get: 70 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB] Get: 71 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB] Get: 72 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 73 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 74 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 75 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 76 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 77 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 78 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 79 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-3 [1631 kB] Get: 80 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 81 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 82 http://deb.debian.org/debian unstable/main i386 debhelper all 13.22 [919 kB] Get: 83 http://deb.debian.org/debian unstable/main i386 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 84 http://deb.debian.org/debian unstable/main i386 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 85 http://deb.debian.org/debian unstable/main i386 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 86 http://deb.debian.org/debian unstable/main i386 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 87 http://deb.debian.org/debian unstable/main i386 python3-inflect all 7.3.1-2 [32.4 kB] Get: 88 http://deb.debian.org/debian unstable/main i386 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 89 http://deb.debian.org/debian unstable/main i386 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 90 http://deb.debian.org/debian unstable/main i386 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 91 http://deb.debian.org/debian unstable/main i386 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 92 http://deb.debian.org/debian unstable/main i386 python3-zipp all 3.21.0-1 [10.6 kB] Get: 93 http://deb.debian.org/debian unstable/main i386 python3-setuptools all 75.6.0-1 [720 kB] Get: 94 http://deb.debian.org/debian unstable/main i386 dh-python all 6.20241217 [113 kB] Get: 95 http://deb.debian.org/debian unstable/main i386 xml-core all 0.19 [20.1 kB] Get: 96 http://deb.debian.org/debian unstable/main i386 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 97 http://deb.debian.org/debian unstable/main i386 fontconfig i386 2.15.0-1.1+b1 [463 kB] Get: 98 http://deb.debian.org/debian unstable/main i386 fonts-lyx all 2.4.2.1-1 [190 kB] Get: 99 http://deb.debian.org/debian unstable/main i386 libblas3 i386 3.12.0-4 [143 kB] Get: 100 http://deb.debian.org/debian unstable/main i386 libpixman-1-0 i386 0.44.0-3 [246 kB] Get: 101 http://deb.debian.org/debian unstable/main i386 libxcb-render0 i386 1.17.0-2+b1 [116 kB] Get: 102 http://deb.debian.org/debian unstable/main i386 libxcb-shm0 i386 1.17.0-2+b1 [105 kB] Get: 103 http://deb.debian.org/debian unstable/main i386 libcairo2 i386 1.18.2-2 [591 kB] Get: 104 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 105 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 106 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 107 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 108 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB] Get: 109 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB] Get: 110 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB] Get: 111 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 112 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 113 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 114 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.11.1-1 [404 kB] Get: 115 http://deb.debian.org/debian unstable/main i386 libcurl4t64 i386 8.11.1-1 [393 kB] Get: 116 http://deb.debian.org/debian unstable/main i386 libdatrie1 i386 0.2.13-3+b1 [39.9 kB] Get: 117 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.22-1 [48.1 kB] Get: 118 http://deb.debian.org/debian unstable/main i386 libexpat1-dev i386 2.6.4-1 [165 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libfribidi0 i386 1.0.16-1 [27.0 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libgfortran5 i386 14.2.0-11 [735 kB] Get: 121 http://deb.debian.org/debian unstable/main i386 libglib2.0-0t64 i386 2.82.4-1 [1572 kB] Get: 122 http://deb.debian.org/debian unstable/main i386 libgraphite2-3 i386 1.3.14-2+b1 [77.8 kB] Get: 123 http://deb.debian.org/debian unstable/main i386 libharfbuzz0b i386 10.1.0-1 [503 kB] Get: 124 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB] Get: 125 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.20+ds-2 [500 kB] Get: 126 http://deb.debian.org/debian unstable/main i386 libice6 i386 2:1.1.1-1 [67.8 kB] Get: 127 http://deb.debian.org/debian unstable/main i386 libimagequant0 i386 2.18.0-1+b2 [36.0 kB] Get: 128 http://deb.debian.org/debian unstable/main i386 libjbig0 i386 2.1-6.1+b2 [32.2 kB] Get: 129 http://deb.debian.org/debian unstable/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 130 http://deb.debian.org/debian unstable/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 131 http://deb.debian.org/debian unstable/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 132 http://deb.debian.org/debian unstable/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 133 http://deb.debian.org/debian unstable/main i386 libjs-sphinxdoc all 8.1.3-2 [30.3 kB] Get: 134 http://deb.debian.org/debian unstable/main i386 libjson-perl all 4.10000-1 [87.5 kB] Get: 135 http://deb.debian.org/debian unstable/main i386 liblapack3 i386 3.12.0-4 [2194 kB] Get: 136 http://deb.debian.org/debian unstable/main i386 liblbfgsb0 i386 3.0+dfsg.4-1+b2 [29.5 kB] Get: 137 http://deb.debian.org/debian unstable/main i386 liblcms2-2 i386 2.16-2 [171 kB] Get: 138 http://deb.debian.org/debian unstable/main i386 liblerc4 i386 4.0.0+ds-5 [191 kB] Get: 139 http://deb.debian.org/debian unstable/main i386 libopenjp2-7 i386 2.5.0-2+b4 [210 kB] Get: 140 http://deb.debian.org/debian unstable/main i386 libthai-data all 0.1.29-2 [168 kB] Get: 141 http://deb.debian.org/debian unstable/main i386 libthai0 i386 0.1.29-2+b1 [50.3 kB] Get: 142 http://deb.debian.org/debian unstable/main i386 libpango-1.0-0 i386 1.55.0+ds-3 [233 kB] Get: 143 http://deb.debian.org/debian unstable/main i386 libpangoft2-1.0-0 i386 1.55.0+ds-3 [58.2 kB] Get: 144 http://deb.debian.org/debian unstable/main i386 libpangocairo-1.0-0 i386 1.55.0+ds-3 [36.2 kB] Get: 145 http://deb.debian.org/debian unstable/main i386 libpaper1 i386 1.1.29+b2 [13.0 kB] Get: 146 http://deb.debian.org/debian unstable/main i386 libpaper-utils i386 1.1.29+b2 [9304 B] Get: 147 http://deb.debian.org/debian unstable/main i386 libpython3.12t64 i386 3.12.8-3 [2171 kB] Get: 148 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 149 http://deb.debian.org/debian unstable/main i386 libpython3.12-dev i386 3.12.8-3 [5296 kB] Get: 150 http://deb.debian.org/debian unstable/main i386 libpython3-dev i386 3.12.7-1 [9988 B] Get: 151 http://deb.debian.org/debian unstable/main i386 libpython3.13-stdlib i386 3.13.1-2 [1981 kB] Get: 152 http://deb.debian.org/debian unstable/main i386 libpython3.13 i386 3.13.1-2 [2199 kB] Get: 153 http://deb.debian.org/debian unstable/main i386 libpython3.13-dev i386 3.13.1-2 [5193 kB] Get: 154 http://deb.debian.org/debian unstable/main i386 libpython3-all-dev i386 3.12.7-1 [1072 B] Get: 155 http://deb.debian.org/debian unstable/main i386 libqhull-r8.0 i386 2020.2-6+b2 [259 kB] Get: 156 http://deb.debian.org/debian unstable/main i386 libraqm0 i386 0.10.2-1 [14.6 kB] Get: 157 http://deb.debian.org/debian unstable/main i386 libsharpyuv0 i386 1.4.0-0.1+b1 [113 kB] Get: 158 http://deb.debian.org/debian unstable/main i386 libsm6 i386 2:1.2.4-1 [35.9 kB] Get: 159 http://deb.debian.org/debian unstable/main i386 libwebp7 i386 1.4.0-0.1+b1 [322 kB] Get: 160 http://deb.debian.org/debian unstable/main i386 libtiff6 i386 4.5.1+git230720-5 [339 kB] Get: 161 http://deb.debian.org/debian unstable/main i386 libwebpdemux2 i386 1.4.0-0.1+b1 [111 kB] Get: 162 http://deb.debian.org/debian unstable/main i386 libwebpmux3 i386 1.4.0-0.1+b1 [125 kB] Get: 163 http://deb.debian.org/debian unstable/main i386 libxslt1.1 i386 1.1.35-1.1+b1 [243 kB] Get: 164 http://deb.debian.org/debian unstable/main i386 libxt6t64 i386 1:1.2.1-1.2+b1 [193 kB] Get: 165 http://deb.debian.org/debian unstable/main i386 libyaml-0-2 i386 0.2.5-1+b2 [56.0 kB] Get: 166 http://deb.debian.org/debian unstable/main i386 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 167 http://deb.debian.org/debian unstable/main i386 python-matplotlib-data all 3.8.3-3 [2731 kB] Get: 168 http://deb.debian.org/debian unstable/main i386 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 169 http://deb.debian.org/debian unstable/main i386 python3.13 i386 3.13.1-2 [740 kB] Get: 170 http://deb.debian.org/debian unstable/main i386 python3-all i386 3.12.7-1 [1052 B] Get: 171 http://deb.debian.org/debian unstable/main i386 python3.12-dev i386 3.12.8-3 [505 kB] Get: 172 http://deb.debian.org/debian unstable/main i386 python3-dev i386 3.12.7-1 [26.1 kB] Get: 173 http://deb.debian.org/debian unstable/main i386 python3.13-dev i386 3.13.1-2 [505 kB] Get: 174 http://deb.debian.org/debian unstable/main i386 python3-all-dev i386 3.12.7-1 [1076 B] Get: 175 http://deb.debian.org/debian unstable/main i386 python3-attr all 24.2.0-1 [68.4 kB] Get: 176 http://deb.debian.org/debian unstable/main i386 python3-babel all 2.16.0-1 [114 kB] Get: 177 http://deb.debian.org/debian unstable/main i386 python3-brotli i386 1.1.0-2+b6 [319 kB] Get: 178 http://deb.debian.org/debian unstable/main i386 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 179 http://deb.debian.org/debian unstable/main i386 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 180 http://deb.debian.org/debian unstable/main i386 python3-charset-normalizer i386 3.4.0-1+b1 [139 kB] Get: 181 http://deb.debian.org/debian unstable/main i386 python3-numpy i386 1:1.26.4+ds-12 [4752 kB] Get: 182 http://deb.debian.org/debian unstable/main i386 python3-contourpy i386 1.3.1-1 [271 kB] Get: 183 http://deb.debian.org/debian unstable/main i386 python3-cycler all 0.12.1-1 [9496 B] Get: 184 http://deb.debian.org/debian unstable/main i386 python3-dateutil all 2.9.0-3 [79.3 kB] Get: 185 http://deb.debian.org/debian unstable/main i386 python3-decorator all 5.1.1-5 [15.1 kB] Get: 186 http://deb.debian.org/debian unstable/main i386 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 187 http://deb.debian.org/debian unstable/main i386 python3-roman all 4.2-1 [10.4 kB] Get: 188 http://deb.debian.org/debian unstable/main i386 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 189 http://deb.debian.org/debian unstable/main i386 python3-tz all 2024.2-1 [31.0 kB] Get: 190 http://deb.debian.org/debian unstable/main i386 python3-platformdirs all 4.3.6-1 [16.6 kB] Get: 191 http://deb.debian.org/debian unstable/main i386 python3-fs all 2.4.16-5.1 [95.2 kB] Get: 192 http://deb.debian.org/debian unstable/main i386 python3-lxml i386 5.3.0-1+b1 [1586 kB] Get: 193 http://deb.debian.org/debian unstable/main i386 python3-lz4 i386 4.4.0+dfsg-1 [25.5 kB] Get: 194 http://deb.debian.org/debian unstable/main i386 python3-scipy i386 1.14.1-3 [20.1 MB] Get: 195 http://deb.debian.org/debian unstable/main i386 python3-mpmath all 1.3.0-1 [419 kB] Get: 196 http://deb.debian.org/debian unstable/main i386 python3-sympy all 1.13.3-1 [4147 kB] Get: 197 http://deb.debian.org/debian unstable/main i386 python3-ufolib2 all 0.17.0+dfsg1-1 [33.0 kB] Get: 198 http://deb.debian.org/debian unstable/main i386 unicode-data all 15.1.0-1 [8547 kB] Get: 199 http://deb.debian.org/debian unstable/main i386 python3-fonttools i386 4.55.0-3 [1593 kB] Get: 200 http://deb.debian.org/debian unstable/main i386 python3-idna all 3.8-2 [41.6 kB] Get: 201 http://deb.debian.org/debian unstable/main i386 python3-imagesize all 1.4.1-1 [6688 B] Get: 202 http://deb.debian.org/debian unstable/main i386 python3-iniconfig all 1.1.1-2 [6396 B] Get: 203 http://deb.debian.org/debian unstable/main i386 python3-markupsafe i386 2.1.5-1+b2 [13.9 kB] Get: 204 http://deb.debian.org/debian unstable/main i386 python3-jinja2 all 3.1.3-1.1 [120 kB] Get: 205 http://deb.debian.org/debian unstable/main i386 python3-kiwisolver i386 1.4.7-2+b1 [83.4 kB] Get: 206 http://deb.debian.org/debian unstable/main i386 python3-pil i386 10.4.0-1+b1 [513 kB] Get: 207 http://deb.debian.org/debian unstable/main i386 python3.12-tk i386 3.12.8-3 [113 kB] Get: 208 http://deb.debian.org/debian unstable/main i386 python3.13-tk i386 3.13.1-2 [104 kB] Get: 209 http://deb.debian.org/debian unstable/main i386 python3-tk i386 3.13.1-1 [9464 B] Get: 210 http://deb.debian.org/debian unstable/main i386 python3-pil.imagetk i386 10.4.0-1+b1 [80.1 kB] Get: 211 http://deb.debian.org/debian unstable/main i386 python3-pyparsing all 3.1.2-1 [146 kB] Get: 212 http://deb.debian.org/debian unstable/main i386 python3-packaging all 24.2-1 [55.3 kB] Get: 213 http://deb.debian.org/debian unstable/main i386 python3-matplotlib i386 3.8.3-3+b1 [5660 kB] Get: 214 http://deb.debian.org/debian unstable/main i386 sphinx-common all 8.1.3-2 [616 kB] Get: 215 http://deb.debian.org/debian unstable/main i386 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 216 http://deb.debian.org/debian unstable/main i386 python3-urllib3 all 2.2.3-4 [112 kB] Get: 217 http://deb.debian.org/debian unstable/main i386 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 218 http://deb.debian.org/debian unstable/main i386 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 219 http://deb.debian.org/debian unstable/main i386 python3-sphinx all 8.1.3-2 [468 kB] Get: 220 http://deb.debian.org/debian unstable/main i386 python3-tabulate all 0.9.0-1 [45.9 kB] Get: 221 http://deb.debian.org/debian unstable/main i386 python3-numpydoc all 1.8.0-1 [51.4 kB] Get: 222 http://deb.debian.org/debian unstable/main i386 python3-pandas-lib i386 2.2.3+dfsg-5+b1 [6860 kB] Get: 223 http://deb.debian.org/debian unstable/main i386 python3-pandas all 2.2.3+dfsg-5 [3096 kB] Get: 224 http://deb.debian.org/debian unstable/main i386 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 225 http://deb.debian.org/debian unstable/main i386 python3-psutil i386 5.9.8-2 [226 kB] Get: 226 http://deb.debian.org/debian unstable/main i386 python3-pysam i386 0.22.1+ds-2+b2 [4429 kB] Get: 227 http://deb.debian.org/debian unstable/main i386 python3-pytest all 8.3.4-1 [250 kB] Get: 228 http://deb.debian.org/debian unstable/main i386 python3-yaml i386 6.0.2-1+b1 [173 kB] Get: 229 http://deb.debian.org/debian unstable/main i386 zip i386 3.0-14 [239 kB] Get: 230 http://deb.debian.org/debian unstable/main i386 unzip i386 6.0-28 [166 kB] Get: 231 http://deb.debian.org/debian unstable/main i386 xdg-utils all 1.2.1-2 [75.8 kB] Get: 232 http://deb.debian.org/debian unstable/main i386 r-base-core i386 4.4.2-1 [28.3 MB] Fetched 183 MB in 2s (90.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:i386. (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 ... 19953 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.8-3_i386.deb ... Unpacking libpython3.12-minimal:i386 (3.12.8-3) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-3_i386.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:i386 (3.12.8-3) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (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 ... 20273 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.7-1_i386.deb ... 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Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:i386. Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ... Unpacking libnsl2:i386 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:i386. Preparing to unpack .../14-libreadline8t64_8.2-6_i386.deb ... Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8.2 to /lib/i386-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8 to /lib/i386-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/i386-linux-gnu/libreadline.so.8.2 to /lib/i386-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:i386 (8.2-6) ... Selecting previously unselected package libpython3.12-stdlib:i386. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_i386.deb ... Unpacking libpython3.12-stdlib:i386 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-3_i386.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../17-libpython3-stdlib_3.12.7-1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.12.7-1) ... Setting up python3-minimal (3.12.7-1) ... 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 ... 21336 files and directories currently installed.) Preparing to unpack .../000-python3_3.12.7-1_i386.deb ... Unpacking python3 (3.12.7-1) ... Selecting previously unselected package libpython3.13-minimal:i386. 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Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-2) ... Setting up python3-numpydoc (1.8.0-1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/python-pybedtools-0.10.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pybedtools_0.10.0-2_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 i386 dpkg-source: info: using options from python-pybedtools-0.10.0/debian/source/options: --extend-diff-ignore=(pybedtools/version.py|docs/source/pybedtools.featurefuncs.*.rst) debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0' /bin/rm -rf fakehome .eggs .pybuild .pytest_cache /bin/rm -rf debian/python3-pybedtools debian/files /bin/rm -rf pybedtools.egg-info /bin/rm -rf pybedtools/scripts/__pycache__/ /bin/rm -rf pybedtools/contrib/__pycache__/ /bin/rm -rf pybedtools/__pycache__/ find pybedtools -name "*.so" -o -name "*.o" | xargs -r rm rm -rf build rm -rf docs/build docs/*.bed docs/*.genome rm -rf dist /bin/rm -rf pybedtools/cbedtools.cpp pybedtools/featurefuncs.cpp find docs/source/autodocs/ -name "*.rst" | xargs -r /bin/rm # dh_auto_clean make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3,sphinxdoc --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running config I: pybuild base:311: python3.12 setup.py config /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0' python3 setup.py cythonize /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running cythonize /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/cbedtools.pxd tree = Parsing.p_module(s, pxd, full_module_name) Compiling pybedtools/cbedtools.pyx because it changed. Compiling pybedtools/featurefuncs.pyx because it changed. [1/2] Cythonizing pybedtools/cbedtools.pyx [2/2] Cythonizing pybedtools/featurefuncs.pyx dh_auto_build I: pybuild base:311: /usr/bin/python3.13 setup.py build /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running build running build_py creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/version.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/parallel.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/logger.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/stats.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/bedtool.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/paths.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/filenames.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/genome_registry.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/settings.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_helpers.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_gzip_support.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_1.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_issues.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_pathlib.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_len_leak.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/regression_tests.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/genomepy_integration.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_cbedtools.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/tfuncs.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_contrib.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_iter.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/plotting.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data running egg_info creating pybedtools.egg-info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt writing manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'pybedtools' warning: no previously-included files matching '__pycache__' found under directory '*' warning: no previously-included files matching '*.py[co]' found under directory '*' adding license file 'LICENSE.txt' writing manifest file 'pybedtools.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/_Window.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/cbedtools.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/cbedtools.pxd -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/cbedtools.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/featurefuncs.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools copying pybedtools/featurefuncs.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/bedFile.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/bedFile.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/fileType.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/fileType.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/gzstream.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/gzstream.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/include/lineFileUtilities.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/include copying pybedtools/test/data/gdc.50.200.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/small.fastq -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/example.narrowPeak -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/x.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/v.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.cram -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/m1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/tag_test2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/genome.fa -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/1000genomes-example.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.vcf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.vcf.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/reads.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/x.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue_121.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/d.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg38-problem.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/bedpe2.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/a.links.html -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/exons.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/expand_test.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/tag_test1.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/venn.b.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/mm9.bed12 -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_tsses.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/y.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.out.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test.fa -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/164.gtf -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/c.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam.bai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/democonfig.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/small.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test/data copying pybedtools/test/gchart-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/mpl-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/prevent_open_file_regression -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_cases.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_merge215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_merge227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_shuffle215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test copying pybedtools/test/test_shuffle227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/test running build_ext building 'pybedtools.cbedtools' extension creating build/temp.linux-i686-cpython-313/pybedtools creating build/temp.linux-i686-cpython-313/pybedtools/include i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/cbedtools.cpp -o build/temp.linux-i686-cpython-313/pybedtools/cbedtools.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/bedFile.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/fileType.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/gzstream.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/pybedtools/cbedtools.o build/temp.linux-i686-cpython-313/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-313/pybedtools/include/fileType.o build/temp.linux-i686-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/cbedtools.cpython-313-i386-linux-gnu.so building 'pybedtools.featurefuncs' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/featurefuncs.cpp -o build/temp.linux-i686-cpython-313/pybedtools/featurefuncs.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/bedFile.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/fileType.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.13 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-313/pybedtools/include/gzstream.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-313/pybedtools/featurefuncs.o build/temp.linux-i686-cpython-313/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-313/pybedtools/include/fileType.o build/temp.linux-i686-cpython-313/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/featurefuncs.cpython-313-i386-linux-gnu.so I: pybuild base:311: /usr/bin/python3 setup.py build /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running build running build_py creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/helpers.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/parallel.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/__init__.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/bedtool.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/filenames.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/genome_registry.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/settings.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_helpers.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/test_1.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_issues.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_pathlib.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/regression_tests.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/genomepy_integration.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/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_iter.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/plotting.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/contrib creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/__init__.py -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data running egg_info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt reading manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'pybedtools' warning: no previously-included files matching '__pycache__' found under directory '*' warning: no previously-included files matching '*.py[co]' found under directory '*' adding license file 'LICENSE.txt' writing manifest file 'pybedtools.egg-info/SOURCES.txt' /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/_Window.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/cbedtools.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/cbedtools.pxd -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/cbedtools.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/featurefuncs.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools copying pybedtools/featurefuncs.pyx -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools creating /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/bedFile.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/bedFile.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/fileType.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/fileType.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/gzstream.cpp -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/gzstream.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/include/lineFileUtilities.h -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/include copying pybedtools/test/data/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/small.fastq -> /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/test_peaks.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/x.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.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/test.fa.fai -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/issue319.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/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.cram -> /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/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/m1.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/a.igv_script -> /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/1000genomes-example.vcf -> /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/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/issue319.vcf.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/reads.bam -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/hg38-base.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/gdc.bed -> /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/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/issue_121.bam -> /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/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/b.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.gff.gz -> /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/d.gff -> /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/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/hg38-problem.bed -> /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/multibamcov_test.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/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/exons.gff -> /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/expand_test.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/venn.b.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/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/hg19.gff -> /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/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/dm3-chr2L-5M-invalid.gff.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/test_tsses.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/issue319.out.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/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.gz -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/c.gff -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/data copying pybedtools/test/data/gdc.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/democonfig.yaml -> /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/gchart-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/mpl-expected.png -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/prevent_open_file_regression -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_cases.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_merge215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_merge227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_shuffle215.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test copying pybedtools/test/test_shuffle227.yaml -> /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test running build_ext building 'pybedtools.cbedtools' extension creating build/temp.linux-i686-cpython-312/pybedtools creating build/temp.linux-i686-cpython-312/pybedtools/include i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-i686-cpython-312/pybedtools/cbedtools.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/pybedtools/cbedtools.o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/cbedtools.cpython-312-i386-linux-gnu.so building 'pybedtools.featurefuncs' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-i686-cpython-312/pybedtools/featurefuncs.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/pybedtools/featurefuncs.o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/featurefuncs.cpython-312-i386-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 creating build/temp.linux-x86_64-cpython-312/pybedtools creating build/temp.linux-x86_64-cpython-312/pybedtools/include i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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/i386-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/cbedtools.cpython-312-i386-linux-gnu.so building 'pybedtools.featurefuncs' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -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/i386-linux-gnu -lstdc++ -lz -o /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/featurefuncs.cpython-312-i386-linux-gnu.so Creating /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/lib/python3.12/site-packages/pybedtools.egg-link (link to .) Adding pybedtools 0.10.0 to easy-install.pth file Installed /build/reproducible-path/python-pybedtools-0.10.0 Processing dependencies for pybedtools==0.10.0 Searching for pysam==0.22.1 Best match: pysam 0.22.1 Adding pysam 0.22.1 to easy-install.pth file Using /usr/lib/python3/dist-packages Searching for numpy==1.26.4 Best match: numpy 1.26.4 Adding numpy 1.26.4 to easy-install.pth file Installing f2py script to /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/bin Installing f2py3 script to /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/bin Installing f2py3.13 script to /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/bin Installing f2py3.12 script to /build/reproducible-path/python-pybedtools-0.10.0/fakehome/.local/bin Using /usr/lib/python3/dist-packages Finished processing dependencies for pybedtools==0.10.0 sphinx-build -N -b html docs/source docs/html Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst [autosummary] generating autosummary for: /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.add_color.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.bedgraph_scale.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.extend_fields.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.five_prime.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.greater_than.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.less_than.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.three_prime.rst building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 48 source files that are out of date updating environment: [new config] 157 added, 0 changed, 0 removed reading sources... [ 1%] 3-brief-examples reading sources... [ 1%] FAQs reading sources... [ 2%] autodoc_source /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/contrib/long_range_interaction.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.annotate reading sources... [ 5%] autodocs/pybedtools.bedtool.BedTool.any_hits reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.at reading sources... [ 7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bed6 reading sources... [ 9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize reading sources... 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[100%] tutorial-contents WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.links' with 'bedtool.BedTool.links'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.igv' with 'bedtool.BedTool.igv'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window_maker' with 'bedtool.BedTool.window_maker'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.groupby' with 'bedtool.BedTool.groupby'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.expand' with 'bedtool.BedTool.expand'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. 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[ 89%] pybedtools.featurefuncs.rename writing output... [ 90%] pybedtools.featurefuncs.three_prime writing output... [ 90%] save-results writing output... [ 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. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history..decorated:28: WARNING: Lexing literal_block 'Tool: bedtools groupby \nVersion: v2.31.1\nSummary: Summarizes a dataset column based upon\n common column groupings. Akin to the SQL "group by" command.\n\nUsage: bedtools groupby -g [group**column(s)] -c [op**column(s)] -o [ops] \n cat [FILE] | bedtools groupby -g [group**column(s)] -c [op**column(s)] -o [ops] \n\nOptions: \n -i Input file. Assumes "stdin" if omitted.\n\n -g -grp Specify the columns (1-based) for the grouping.\n The columns must be comma separated.\n - Default: 1,2,3\n\n -c -opCols Specify the column (1-based) that should be summarized.\n - Required.\n\n -o -ops Specify the operation that should be applied to opCol.\n Valid operations:\n sum, count, count**distinct, min, max,\n mean, median, mode, antimode,\n stdev, sstdev (sample standard dev.),\n collapse (i.e., print a comma separated list (duplicates allowed)), \n distinct (i.e., print a comma separated list (NO duplicates allowed)), \n distinct**sort**num (as distinct, but sorted numerically, ascending), \n distinct**sort**num**desc (as distinct, but sorted numerically, descending), \n concat (i.e., merge values into a single, non-delimited string), \n freqdesc (i.e., print desc. list of values:freq)\n freqasc (i.e., print asc. list of values:freq)\n first (i.e., print first value)\n last (i.e., print last value)\n - Default: sum\n\n If there is only column, but multiple operations, all operations will be\n applied on that column. Likewise, if there is only one operation, but\n multiple columns, that operation will be applied to all columns.\n Otherwise, the number of columns must match the the number of operations,\n and will be applied in respective order.\n E.g., "-c 5,4,6 -o sum,mean,count" will give the sum of column 5,\n the mean of column 4, and the count of column 6.\n The order of output columns will match the ordering given in the command.\n\n -full Print all columns from input file. The first line in the group is used.\n Default: print only grouped columns.\n\n -inheader Input file has a header line - the first line will be ignored.\n\n -outheader Print header line in the output, detailing the column names. \n If the input file has headers (-inheader), the output file\n will use the input\'s column names.\n If the input file has no headers, the output file\n will use "col**1", "col**2", etc. as the column names.\n\n -header same as \'-inheader -outheader\'\n\n -ignorecase Group values regardless of upper/lower case.\n\n -prec Sets the decimal precision for output (Default: 5)\n\n -delim Specify a custom delimiter for the collapse operations.\n - Example: -delim "|"\n - Default: ",".\n\nExamples: \n $ cat ex1.out\n chr1 10 20 A chr1 15 25 B.1 1000 ATAT\n chr1 10 20 A chr1 25 35 B.2 10000 CGCG\n\n $ groupBy -i ex1.out -g 1,2,3,4 -c 9 -o sum\n chr1 10 20 A 11000\n\n $ groupBy -i ex1.out -grp 1,2,3,4 -opCols 9,9 -ops sum,max\n chr1 10 20 A 11000 10000\n\n $ groupBy -i ex1.out -g 1,2,3,4 -c 8,9 -o collapse,mean\n chr1 10 20 A B.1,B.2, 5500\n\n $ cat ex1.out | groupBy -g 1,2,3,4 -c 8,9 -o collapse,mean\n chr1 10 20 A B.1,B.2, 5500\n\n $ cat ex1.out | groupBy -g 1,2,3,4 -c 10 -o concat\n chr1 10 20 A ATATCGCG\n\nNotes: \n (1) The input file/stream should be sorted/grouped by the -grp. columns\n (2) If -i is unspecified, input is assumed to come from stdin.' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history..decorated:20: WARNING: Lexing literal_block 'Tool: bedtools overlap (aka getOverlap)\nVersion: v2.31.1\nSummary: Computes the amount of overlap (positive values)\n or distance (negative values) between genome features\n and reports the result at the end of the same line.\n\nOptions: \n -i Input file. Use "stdin" for pipes.\n\n -cols Specify the columns (1-based) for the starts and ends of the\n features for which you\'d like to compute the overlap/distance.\n The columns must be listed in the following order: \n\n start1,end1,start2,end2\n\nExample: \n $ bedtools window -a A.bed -b B.bed -w 10\n chr1 10 20 A chr1 15 25 B\n chr1 10 20 C chr1 25 35 D\n\n $ bedtools window -a A.bed -b B.bed -w 10 | bedtools overlap -i stdin -cols 2,3,6,7\n chr1 10 20 A chr1 15 25 B 5\n chr1 10 20 C chr1 25 35 D -5' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py:docstring of pybedtools.bedtool.BedTool._log_to_history..decorated:16: WARNING: Lexing literal_block 'Tool: bedtools makewindows\nVersion: v2.31.1\nSummary: Makes adjacent or sliding windows across a genome or BED file.\n\nUsage: bedtools makewindows [OPTIONS] [-g OR -b ]\n [ -w OR -n ]\n\nInput Options: \n -g \n Genome file size (see notes below).\n Windows will be created for each chromosome in the file.\n\n -b \n BED file (with chrom,start,end fields).\n Windows will be created for each interval in the file.\n\nWindows Output Options: \n -w \n Divide each input interval (either a chromosome or a BED interval)\n to fixed-sized windows (i.e. same number of nucleotide in each window).\n Can be combined with -s \n\n -s \n Step size: i.e., how many base pairs to step before\n creating a new window. Used to create "sliding" windows.\n - Defaults to window size (non-sliding windows).\n\n -n \n Divide each input interval (either a chromosome or a BED interval)\n to fixed number of windows (i.e. same number of windows, with\n varying window sizes).\n\n -reverse\n Reverse numbering of windows in the output, i.e. report \n windows in decreasing order\n\nID Naming Options: \n -i src|winnum|srcwinnum\n The default output is 3 columns: chrom, start, end .\n With this option, a name column will be added.\n "-i src" - use the source interval\'s name.\n "-i winnum" - use the window number as the ID (e.g. 1,2,3,4...).\n "-i srcwinnum" - use the source interval\'s name with the window number.\n See below for usage examples.\n\nNotes: \n (1) The genome file should tab delimited and structured as follows:\n \n\n For example, Human (hg19):\n chr1 249250621\n chr2 243199373\n ...\n chr18**gl000207**random 4262\n\nTip 1. Use samtools faidx to create a genome file from a FASTA: \n One can the samtools faidx command to index a FASTA file.\n The resulting .fai index is suitable as a genome file, \n as bedtools will only look at the first two, relevant columns\n of the .fai file.\n\n For example:\n samtools faidx GRCh38.fa\n bedtools makewindows -w 100 -g GRCh38.fa.fai\n\nTip 2. Use UCSC Table Browser to create a genome file: \n One can use the UCSC Genome Browser\'s MySQL database to extract\n chromosome sizes. For example, H. sapiens:\n\n mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \\\n "select chrom, size from hg19.chromInfo" > hg19.genome\n\nExamples: \n # Divide the human genome into windows of 1MB:\n $ bedtools makewindows -g hg19.txt -w 1000000\n chr1 0 1000000\n chr1 1000000 2000000\n chr1 2000000 3000000\n chr1 3000000 4000000\n chr1 4000000 5000000\n ...\n\n # Divide the human genome into sliding (=overlapping) windows of 1MB, with 500KB overlap:\n $ bedtools makewindows -g hg19.txt -w 1000000 -s 500000\n chr1 0 1000000\n chr1 500000 1500000\n chr1 1000000 2000000\n chr1 1500000 2500000\n chr1 2000000 3000000\n ...\n\n # Divide each chromosome in human genome to 1000 windows of equal size:\n $ bedtools makewindows -g hg19.txt -n 1000\n chr1 0 249251\n chr1 249251 498502\n chr1 498502 747753\n chr1 747753 997004\n chr1 997004 1246255\n ...\n\n # Divide each interval in the given BED file into 10 equal-sized windows:\n $ cat input.bed\n chr5 60000 70000\n chr5 73000 90000\n chr5 100000 101000\n $ bedtools makewindows -b input.bed -n 10\n chr5 60000 61000\n chr5 61000 62000\n chr5 62000 63000\n chr5 63000 64000\n chr5 64000 65000\n ...\n\n # Add a name column, based on the window number: \n $ cat input.bed\n chr5 60000 70000 AAA\n chr5 73000 90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i winnum\n chr5 60000 63334 1\n chr5 63334 66668 2\n chr5 66668 70000 3\n chr5 73000 78667 1\n chr5 78667 84334 2\n chr5 84334 90000 3\n chr5 100000 100334 1\n chr5 100334 100668 2\n chr5 100668 101000 3\n ...\n\n # Reverse window numbers: \n $ cat input.bed\n chr5 60000 70000 AAA\n chr5 73000 90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i winnum -reverse\n chr5 60000 63334 3\n chr5 63334 66668 2\n chr5 66668 70000 1\n chr5 73000 78667 3\n chr5 78667 84334 2\n chr5 84334 90000 1\n chr5 100000 100334 3\n chr5 100334 100668 2\n chr5 100668 101000 1\n ...\n\n # Add a name column, based on the source ID + window number: \n $ cat input.bed\n chr5 60000 70000 AAA\n chr5 73000 90000 BBB\n chr5 100000 101000 CCC\n $ bedtools makewindows -b input.bed -n 3 -i srcwinnum\n chr5 60000 63334 AAA**1\n chr5 63334 66668 AAA**2\n chr5 66668 70000 AAA**3\n chr5 73000 78667 BBB**1\n chr5 78667 84334 BBB**2\n chr5 84334 90000 BBB**3\n chr5 100000 100334 CCC**1\n chr5 100334 100668 CCC**2\n chr5 100668 101000 CCC**3\n ...' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/default-arguments.rst:35: WARNING: Lexing literal_block '$ intersectBed -a a.bed -b b.bed -u > tmpfile' as "python" resulted in an error at token: '$'. Retrying in relaxed mode. [misc.highlighting_failure] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-design-principles.rst:120: WARNING: unknown option: 'mergeBed -i' [ref.option] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-design-principles.rst:127: WARNING: unknown option: '-i' [ref.option] generating indices... genindex py-modindex done highlighting module code... [ 8%] pybedtools highlighting module code... [ 15%] pybedtools.bedtool highlighting module code... [ 23%] pybedtools.cbedtools highlighting module code... [ 31%] pybedtools.contrib.bigbed highlighting module code... [ 38%] pybedtools.contrib.bigwig highlighting module code... [ 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_3.13_pybedtools/build/pybedtools/test/ ; python3 /build/reproducible-path/python-pybedtools-0.10.0/setup.py install --user ; export HOME=/build/reproducible-path/python-pybedtools-0.10.0/fakehome /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` and ``easy_install``. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://github.com/pypa/setuptools/issues/917 for details. ******************************************************************************** !! self.initialize_options() running bdist_egg running egg_info writing pybedtools.egg-info/PKG-INFO writing dependency_links to pybedtools.egg-info/dependency_links.txt writing requirements to pybedtools.egg-info/requires.txt writing top-level names to pybedtools.egg-info/top_level.txt reading manifest file 'pybedtools.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.c' under directory 'pybedtools' warning: no previously-included files matching '__pycache__' found under directory '*' warning: no previously-included files matching '*.py[co]' found under directory '*' adding license file 'LICENSE.txt' writing manifest file 'pybedtools.egg-info/SOURCES.txt' installing library code to build/bdist.linux-i686/egg running install_lib running build_py creating build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/helpers.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/version.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/parallel.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/logger.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/__init__.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/stats.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/bedtool.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/paths.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/filenames.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/genome_registry.py -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/settings.py -> build/lib.linux-i686-cpython-312/pybedtools creating build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_helpers.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_gzip_support.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_1.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_issues.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_pathlib.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_len_leak.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/regression_tests.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/__init__.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/genomepy_integration.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_cbedtools.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/tfuncs.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_contrib.py -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_iter.py -> build/lib.linux-i686-cpython-312/pybedtools/test creating build/lib.linux-i686-cpython-312/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib copying pybedtools/contrib/__init__.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib copying pybedtools/contrib/plotting.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib copying pybedtools/contrib/bigbed.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> build/lib.linux-i686-cpython-312/pybedtools/contrib creating build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/__init__.py -> build/lib.linux-i686-cpython-312/pybedtools/test/data /usr/lib/python3/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration. !! ******************************************************************************** ############################ # Package would be ignored # ############################ Python recognizes 'pybedtools.include' as an importable package[^1], but it is absent from setuptools' `packages` configuration. This leads to an ambiguous overall configuration. If you want to distribute this package, please make sure that 'pybedtools.include' is explicitly added to the `packages` configuration field. Alternatively, you can also rely on setuptools' discovery methods (for example by using `find_namespace_packages(...)`/`find_namespace:` instead of `find_packages(...)`/`find:`). You can read more about "package discovery" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html If you don't want 'pybedtools.include' to be distributed and are already explicitly excluding 'pybedtools.include' via `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, you can try to use `exclude_package_data`, or `include-package-data=False` in combination with a more fine grained `package-data` configuration. You can read more about "package data files" on setuptools documentation page: - https://setuptools.pypa.io/en/latest/userguide/datafiles.html [^1]: For Python, any directory (with suitable naming) can be imported, even if it does not contain any `.py` files. On the other hand, currently there is no concept of package data directory, all directories are treated like packages. ******************************************************************************** !! check.warn(importable) copying pybedtools/_Window.pyx -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/cbedtools.cpp -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/cbedtools.pxd -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/cbedtools.pyx -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/featurefuncs.cpp -> build/lib.linux-i686-cpython-312/pybedtools copying pybedtools/featurefuncs.pyx -> build/lib.linux-i686-cpython-312/pybedtools creating build/lib.linux-i686-cpython-312/pybedtools/include copying pybedtools/include/bedFile.cpp -> build/lib.linux-i686-cpython-312/pybedtools/include copying pybedtools/include/bedFile.h -> build/lib.linux-i686-cpython-312/pybedtools/include copying pybedtools/include/fileType.cpp -> build/lib.linux-i686-cpython-312/pybedtools/include copying pybedtools/include/fileType.h -> build/lib.linux-i686-cpython-312/pybedtools/include copying pybedtools/include/gzstream.cpp -> build/lib.linux-i686-cpython-312/pybedtools/include copying pybedtools/include/gzstream.h -> build/lib.linux-i686-cpython-312/pybedtools/include copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-i686-cpython-312/pybedtools/include copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/small.fastq -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/x.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/test.fa.fai -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue319.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/v.vcf -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.cram -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/m1.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/genome.fa -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/bedpe.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/reads.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/x.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue_121.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/b.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/a.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/d.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/a.links.html -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/exons.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/expand_test.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/venn.b.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/hg19.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/y.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/test.fa -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/164.gtf -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/c.gff -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/data/small.bam -> build/lib.linux-i686-cpython-312/pybedtools/test/data copying pybedtools/test/gchart-expected.png -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/mpl-expected.png -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_cases.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_merge215.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_merge227.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_shuffle215.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test copying pybedtools/test/test_shuffle227.yaml -> build/lib.linux-i686-cpython-312/pybedtools/test running build_ext building 'pybedtools.cbedtools' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/cbedtools.cpp -o build/temp.linux-i686-cpython-312/pybedtools/cbedtools.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/pybedtools/cbedtools.o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o build/lib.linux-i686-cpython-312/pybedtools/cbedtools.cpython-312-i386-linux-gnu.so building 'pybedtools.featurefuncs' extension i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/featurefuncs.cpp -o build/temp.linux-i686-cpython-312/pybedtools/featurefuncs.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/bedFile.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/fileType.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipybedtools/include/ -I/usr/include/python3.12 -c pybedtools/include/gzstream.cpp -o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/python-pybedtools-0.10.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-i686-cpython-312/pybedtools/featurefuncs.o build/temp.linux-i686-cpython-312/pybedtools/include/bedFile.o build/temp.linux-i686-cpython-312/pybedtools/include/fileType.o build/temp.linux-i686-cpython-312/pybedtools/include/gzstream.o -L/usr/lib/i386-linux-gnu -lstdc++ -lz -o build/lib.linux-i686-cpython-312/pybedtools/featurefuncs.cpython-312-i386-linux-gnu.so creating build/bdist.linux-i686/egg creating build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/cbedtools.pyx -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/featurefuncs.pyx -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/helpers.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/_Window.pyx -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/version.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/parallel.py -> build/bdist.linux-i686/egg/pybedtools creating build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_merge215.yaml -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_helpers.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/mpl-expected.png -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/gchart-expected.png -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_gzip_support.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_1.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_issues.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_pathlib.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_len_leak.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/regression_tests.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/__init__.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/genomepy_integration.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_cbedtools.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_merge227.yaml -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_cases.yaml -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/tfuncs.py -> build/bdist.linux-i686/egg/pybedtools/test creating build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/small.fastq -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/x.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test.fa.fai -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/venn.c.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/issue319.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/v.vcf -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.cram -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.gff -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/m1.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/a.igv_script -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/genome.fa -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/bedpe.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/reads.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/x.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/issue_121.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/b.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/a.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/d.gff -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/__init__.py -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/a.links.html -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/exons.gff -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/expand_test.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/venn.b.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/hg19.gff -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/y.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/test.fa -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/164.gtf -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/c.gff -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/data/small.bam -> build/bdist.linux-i686/egg/pybedtools/test/data copying build/lib.linux-i686-cpython-312/pybedtools/test/test_contrib.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_iter.py -> build/bdist.linux-i686/egg/pybedtools/test copying build/lib.linux-i686-cpython-312/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-i686/egg/pybedtools/test creating build/bdist.linux-i686/egg/pybedtools/contrib copying build/lib.linux-i686-cpython-312/pybedtools/contrib/bigwig.py -> build/bdist.linux-i686/egg/pybedtools/contrib copying build/lib.linux-i686-cpython-312/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-i686/egg/pybedtools/contrib copying build/lib.linux-i686-cpython-312/pybedtools/contrib/__init__.py -> build/bdist.linux-i686/egg/pybedtools/contrib copying build/lib.linux-i686-cpython-312/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-i686/egg/pybedtools/contrib copying build/lib.linux-i686-cpython-312/pybedtools/contrib/plotting.py -> build/bdist.linux-i686/egg/pybedtools/contrib copying build/lib.linux-i686-cpython-312/pybedtools/contrib/bigbed.py -> build/bdist.linux-i686/egg/pybedtools/contrib copying build/lib.linux-i686-cpython-312/pybedtools/contrib/venn_maker.py -> build/bdist.linux-i686/egg/pybedtools/contrib creating build/bdist.linux-i686/egg/pybedtools/include copying build/lib.linux-i686-cpython-312/pybedtools/include/fileType.cpp -> build/bdist.linux-i686/egg/pybedtools/include copying build/lib.linux-i686-cpython-312/pybedtools/include/gzstream.h -> build/bdist.linux-i686/egg/pybedtools/include copying build/lib.linux-i686-cpython-312/pybedtools/include/bedFile.cpp -> build/bdist.linux-i686/egg/pybedtools/include copying build/lib.linux-i686-cpython-312/pybedtools/include/bedFile.h -> build/bdist.linux-i686/egg/pybedtools/include copying build/lib.linux-i686-cpython-312/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-i686/egg/pybedtools/include copying build/lib.linux-i686-cpython-312/pybedtools/include/gzstream.cpp -> build/bdist.linux-i686/egg/pybedtools/include copying build/lib.linux-i686-cpython-312/pybedtools/include/fileType.h -> build/bdist.linux-i686/egg/pybedtools/include copying build/lib.linux-i686-cpython-312/pybedtools/featurefuncs.cpp -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/logger.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/cbedtools.cpython-312-i386-linux-gnu.so -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/cbedtools.cpp -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/__init__.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/stats.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/bedtool.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/paths.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/filenames.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/genome_registry.py -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/featurefuncs.cpython-312-i386-linux-gnu.so -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/cbedtools.pxd -> build/bdist.linux-i686/egg/pybedtools copying build/lib.linux-i686-cpython-312/pybedtools/settings.py -> build/bdist.linux-i686/egg/pybedtools byte-compiling build/bdist.linux-i686/egg/pybedtools/helpers.py to helpers.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/version.py to version.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/parallel.py to parallel.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_helpers.py to test_helpers.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_gzip_support.py to test_gzip_support.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_1.py to test_1.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_issues.py to test_issues.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_pathlib.py to test_pathlib.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_len_leak.py to test_len_leak.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/regression_tests.py to regression_tests.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/genomepy_integration.py to genomepy_integration.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_cbedtools.py to test_cbedtools.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/tfuncs.py to tfuncs.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/data/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_contrib.py to test_contrib.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/test/test_iter.py to test_iter.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/contrib/bigwig.py to bigwig.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/contrib/long_range_interaction.py to long_range_interaction.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/contrib/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/contrib/intersection_matrix.py to intersection_matrix.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/contrib/plotting.py to plotting.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/contrib/bigbed.py to bigbed.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/contrib/venn_maker.py to venn_maker.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/logger.py to logger.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/__init__.py to __init__.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/stats.py to stats.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/bedtool.py to bedtool.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/paths.py to paths.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/filenames.py to filenames.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/genome_registry.py to genome_registry.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/settings.py to settings.cpython-312.pyc creating stub loader for pybedtools/cbedtools.cpython-312-i386-linux-gnu.so creating stub loader for pybedtools/featurefuncs.cpython-312-i386-linux-gnu.so byte-compiling build/bdist.linux-i686/egg/pybedtools/cbedtools.py to cbedtools.cpython-312.pyc byte-compiling build/bdist.linux-i686/egg/pybedtools/featurefuncs.py to featurefuncs.cpython-312.pyc creating build/bdist.linux-i686/egg/EGG-INFO copying pybedtools.egg-info/PKG-INFO -> build/bdist.linux-i686/egg/EGG-INFO copying pybedtools.egg-info/SOURCES.txt -> build/bdist.linux-i686/egg/EGG-INFO copying pybedtools.egg-info/dependency_links.txt -> build/bdist.linux-i686/egg/EGG-INFO copying pybedtools.egg-info/not-zip-safe -> build/bdist.linux-i686/egg/EGG-INFO copying pybedtools.egg-info/requires.txt -> build/bdist.linux-i686/egg/EGG-INFO copying pybedtools.egg-info/top_level.txt -> build/bdist.linux-i686/egg/EGG-INFO writing build/bdist.linux-i686/egg/EGG-INFO/native_libs.txt creating dist creating 'dist/pybedtools-0.10.0-py3.12-linux-i686.egg' and adding 'build/bdist.linux-i686/egg' to it removing 'build/bdist.linux-i686/egg' (and everything under it) Processing pybedtools-0.10.0-py3.12-linux-i686.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-i686.egg Extracting pybedtools-0.10.0-py3.12-linux-i686.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-i686.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-i686.egg' Using /usr/lib/python3/dist-packages Searching for numpy==1.26.4 Best match: numpy 1.26.4 Adding numpy 1.26.4 to easy-install.pth file Installing f2py script to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/bin Installing f2py3 script to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/bin Installing f2py3.13 script to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/bin Installing f2py3.12 script to /build/reproducible-path/python-pybedtools-0.10.0/debian/.debhelper/generated/_source/home/.local/bin Using /usr/lib/python3/dist-packages Finished processing dependencies for pybedtools==0.10.0 I: pybuild base:311: cd /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build; python3.13 -m pytest -k "not test_chromsizes" ============================= test session starts ============================== platform linux -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build configfile: pyproject.toml plugins: typeguard-4.4.1 collected 511 items / 2 deselected / 509 selected pybedtools/test/test_1.py .............................................. [ 9%] .......................x..x.x...... [ 15%] pybedtools/test/test_cbedtools.py ...................................... [ 23%] . [ 23%] pybedtools/test/test_contrib.py .. [ 23%] pybedtools/test/test_gzip_support.py ........ [ 25%] pybedtools/test/test_helpers.py ...... [ 26%] pybedtools/test/test_issues.py ......................................... [ 34%] .. [ 35%] pybedtools/test/test_iter.py ........................................... [ 43%] ........................................................................ [ 57%] ........................................................................ [ 71%] ........................................................................ [ 86%] .................................................................... [ 99%] pybedtools/test/test_pathlib.py ... [100%] ================ 506 passed, 2 deselected, 3 xfailed in 16.20s ================= I: pybuild pybuild:334: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; make clean doctest make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0/docs' rm -rf build/* source/autodocs/*.rst sphinx-build -b doctest -d build/doctrees source build/doctest Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst [autosummary] generating autosummary for: /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.filenames.example_filename.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.filenames.list_example_files.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.chromsizes.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.chromsizes_to_file.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.cleanup.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.get_chromsizes_from_ucsc.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.get_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_bedtools_path.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst building [mo]: targets for 0 po files that are out of date writing output... building [doctest]: targets for 48 source files that are out of date updating environment: [new config] 157 added, 0 changed, 0 removed reading sources... [ 1%] 3-brief-examples reading sources... [ 1%] FAQs reading sources... [ 2%] autodoc_source /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/contrib/long_range_interaction.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.annotate reading sources... [ 5%] autodocs/pybedtools.bedtool.BedTool.any_hits reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.at reading sources... [ 7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bed6 reading sources... [ 9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize reading sources... 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[100%] tutorial-contents WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. 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[autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.moveto' with 'bedtool.BedTool.moveto'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cat' with 'bedtool.BedTool.cat'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.at' with 'bedtool.BedTool.at'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.absolute_distance' with 'bedtool.BedTool.absolute_distance'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cut' with 'bedtool.BedTool.cut'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. 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[autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.save_seqs' with 'bedtool.BedTool.save_seqs'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.seq' with 'bedtool.BedTool.seq'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.liftover' with 'bedtool.BedTool.liftover'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.colormap_normalize' with 'bedtool.BedTool.colormap_normalize'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.relative_distance' with 'bedtool.BedTool.relative_distance'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.example_bedtool' with 'bedtool.example_bedtool'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.list_example_files' with 'filenames.list_example_files'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.example_filename' with 'filenames.example_filename'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.Interval' with 'cbedtools.Interval'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.create_interval_from_list' with 'cbedtools.create_interval_from_list'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_bedtools_path' with 'helpers.set_bedtools_path'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_tempdir' with 'helpers.get_tempdir'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_tempdir' with 'helpers.set_tempdir'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.cleanup' with 'helpers.cleanup'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.debug_mode' with 'debug_mode'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_chromsizes_from_ucsc' with 'helpers.get_chromsizes_from_ucsc'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes' with 'helpers.chromsizes'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes_to_file' with 'helpers.chromsizes_to_file'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.parallel.parallel_apply' with 'parallel.parallel_apply'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.Track' with 'contrib.plotting.Track'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.TrackCollection' with 'contrib.plotting.TrackCollection'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_heatmap' with 'contrib.plotting.binary_heatmap'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_summary' with 'contrib.plotting.binary_summary'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.BedToolsDemo' with 'contrib.plotting.BedToolsDemo'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.ConfiguredBedToolsDemo' with 'contrib.plotting.ConfiguredBedToolsDemo'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bam_to_bigwig' with 'contrib.bigwig.bam_to_bigwig'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bedgraph_to_bigwig' with 'contrib.bigwig.bedgraph_to_bigwig'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.wig_to_bigwig' with 'contrib.bigwig.wig_to_bigwig'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed' with 'contrib.bigbed.bigbed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed_to_bed' with 'contrib.bigbed.bigbed_to_bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.IntersectionMatrix' with 'contrib.IntersectionMatrix'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker' with 'contrib.venn_maker'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.venn_maker' with 'contrib.venn_maker.venn_maker'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.cis_trans_interactions' with 'contrib.long_range_interaction.cis_trans_interactions'. [autosummary.import_cycle] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy". [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.normalized_to_length /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename done preparing documents... done copying assets... copying assets: done running tests... Document: autodocs/pybedtools.bedtool.BedTool.annotate ------------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.cat ------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.complement -------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.count --------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.coverage ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.cut ------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.each -------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.field_count --------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.file_type ------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.filter ---------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.flank --------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.genome_coverage ------------------------------------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.groupby ----------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.head -------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.mask_fasta -------------------------------------------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.merge --------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.moveto ---------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.overlap ----------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.random ---------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.randomintersection ---------------------------------------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.randomstats --------------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.remove_invalid ------------------------------------------------------------ 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.save_seqs ------------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.saveas ---------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.sequence ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.set_chromsizes ------------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.shuffle ----------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.sort -------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.subtract ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.total_coverage ------------------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.with_attrs -------------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.cbedtools.Interval ------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.cbedtools.create_interval_from_list ----------------------------------------------------------------- 1 items passed all tests: 1 tests in default 1 tests in 1 items. 1 passed and 0 failed. Test passed. Document: autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions ----------------------------------------------------------------------------------- ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: iterator, n, extra = tag_bedpe(bedpe, queries) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in iterator, n, extra = tag_bedpe(bedpe, queries) ^^^^^^^^^ NameError: name 'tag_bedpe' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: for (label, group1, group2) in iterator: group1 = sorted(group1, key=lambda x: str(x)) group2 = sorted(group2, key=lambda x: str(x)) for i in group1: print(i, end='') # doctest: +NORMALIZE_WHITESPACE for i in group2: print(i, end='') # doctest: +NORMALIZE_WHITESPACE Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in for (label, group1, group2) in iterator: ^^^^^^^^ NameError: name 'iterator' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks}) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks}) ^^^^^^^^^ NameError: name 'tag_bedpe' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: df = cis_trans_interactions(iterator, n, extra) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in df = cis_trans_interactions(iterator, n, extra) ^^^^^^^^^^^^^^^^^^^^^^ NameError: name 'cis_trans_interactions' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: print(df.sort_values(list(df.columns)).reset_index(drop=True)) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(df.sort_values(list(df.columns)).reset_index(drop=True)) ^^ NameError: name 'df' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: print((df[df.target_label == 'tss']).sort_values(list(df.columns)).reset_index(drop=True)) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in print((df[df.target_label == 'tss']).sort_values(list(df.columns)).reset_index(drop=True)) ^^ NameError: name 'df' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: assert set(df.loc[df.target_name == 'gene2', 'distal_name']).difference('.') == set([u'gene1', u'peak1']) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in assert set(df.loc[df.target_name == 'gene2', 'distal_name']).difference('.') == set([u'gene1', u'peak1']) ^^ NameError: name 'df' is not defined ********************************************************************** 1 items had failures: 7 of 18 in default 18 tests in 1 items. 11 passed and 7 failed. ***Test Failed*** 7 failures. Document: autodocs/pybedtools.contrib.plotting.Track ---------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.filenames.list_example_files ---------------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.helpers.chromsizes ------------------------------------------------ 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.parallel.parallel_apply ----------------------------------------------------- 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: default-arguments --------------------------- 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: each -------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: filtering ------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: history ----------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: intersections ----------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: intervals ------------------- 1 items passed all tests: 50 tests in default 50 tests in 1 items. 50 passed and 0 failed. Test passed. Document: piping ---------------- 1 items passed all tests: 17 tests in default 17 tests in 1 items. 17 passed and 0 failed. Test passed. Document: save-results ---------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: topical-bam --------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-create-a-bedtool ---------------------------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-design-principles ----------------------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-genome ------------------------ 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: topical-iterators --------------------------- 1 items passed all tests: 20 tests in default 20 tests in 1 items. 20 passed and 0 failed. Test passed. Document: topical-low-level-ops ------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: topical-random ------------------------ 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-saving ------------------------ 1 items passed all tests: 14 tests in default 14 tests in 1 items. 14 passed and 0 failed. Test passed. Doctest summary =============== 387 tests 7 failures in tests 0 failures in setup code 0 failures in cleanup code build finished with problems, 126 warnings. make[1]: *** [Makefile:137: doctest] Error 1 make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0/docs' E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; make clean doctest I: pybuild pybuild:308: cp /build/reproducible-path/python-pybedtools-0.10.0/debian/mpl-expected.png /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build/pybedtools/test/ ; python3 /build/reproducible-path/python-pybedtools-0.10.0/setup.py install --user ; export HOME=/build/reproducible-path/python-pybedtools-0.10.0/fakehome /build/reproducible-path/python-pybedtools-0.10.0/setup.py:55: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import pkg_resources /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level' warnings.warn(msg) running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() error: can't combine user with prefix, exec_prefix/home, or install_(plat)base I: pybuild base:311: cd /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build; python3.12 -m pytest -k "not test_chromsizes" ============================= test session starts ============================== platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 rootdir: /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.12_pybedtools/build configfile: pyproject.toml plugins: typeguard-4.4.1 collected 511 items / 2 deselected / 509 selected pybedtools/test/test_1.py .............................................. [ 9%] .......................x..x.x...... [ 15%] pybedtools/test/test_cbedtools.py ...................................... [ 23%] . [ 23%] pybedtools/test/test_contrib.py .. [ 23%] pybedtools/test/test_gzip_support.py ........ [ 25%] pybedtools/test/test_helpers.py ...... [ 26%] pybedtools/test/test_issues.py ......................................... [ 34%] .. [ 35%] pybedtools/test/test_iter.py ........................................... [ 43%] ........................................................................ [ 57%] ........................................................................ [ 71%] ........................................................................ [ 86%] .................................................................... [ 99%] pybedtools/test/test_pathlib.py ... [100%] ================ 506 passed, 2 deselected, 3 xfailed in 16.24s ================= I: pybuild pybuild:334: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; make clean doctest make[1]: Entering directory '/build/reproducible-path/python-pybedtools-0.10.0/docs' rm -rf build/* source/autodocs/*.rst sphinx-build -b doctest -d build/doctrees source build/doctest Running Sphinx v8.1.3 loading translations [en]... done making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. [autosummary] generating autosummary for: 3-brief-examples.rst, FAQs.rst, autodoc_source.rst, changes.rst, create-a-bedtool-tutorial.rst, default-arguments.rst, each.rst, filtering.rst, flow-of-commands.rst, history.rst, ..., topical-create-a-bedtool.rst, topical-design-principles.rst, topical-documentation-contents.rst, topical-genome.rst, topical-iterators.rst, topical-low-level-ops.rst, topical-random.rst, topical-saving.rst, topical-wrapping.rst, tutorial-contents.rst [autosummary] generating autosummary for: /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.all_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.annotate.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.any_hits.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.at.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_bed.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bam_to_fastq.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bed6.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam.rst, ..., /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.filenames.example_filename.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.filenames.list_example_files.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.chromsizes.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.chromsizes_to_file.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.cleanup.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.get_chromsizes_from_ucsc.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.get_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_bedtools_path.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.helpers.set_tempdir.rst, /build/reproducible-path/python-pybedtools-0.10.0/docs/source/autodocs/pybedtools.parallel.parallel_apply.rst building [mo]: targets for 0 po files that are out of date writing output... building [doctest]: targets for 48 source files that are out of date updating environment: [new config] 157 added, 0 changed, 0 removed reading sources... [ 1%] 3-brief-examples reading sources... [ 1%] FAQs reading sources... [ 2%] autodoc_source /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/contrib/long_range_interaction.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.annotate reading sources... [ 5%] autodocs/pybedtools.bedtool.BedTool.any_hits reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.at reading sources... [ 7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bed6 reading sources... [ 9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize reading sources... 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[ 30%] autodocs/pybedtools.bedtool.BedTool.overlap reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence reading sources... [ 33%] autodocs/pybedtools.bedtool.BedTool.random reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op reading sources... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset /usr/lib/python3/dist-packages/numpydoc/docscrape.py:421: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/pybedtools/bedtool.py. self[section] = content reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection reading sources... 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[100%] tutorial-contents WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.intersect' with 'bedtool.BedTool.intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window' with 'bedtool.BedTool.window'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.closest' with 'bedtool.BedTool.closest'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.coverage' with 'bedtool.BedTool.coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.map' with 'bedtool.BedTool.map'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.genome_coverage' with 'bedtool.BedTool.genome_coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.merge' with 'bedtool.BedTool.merge'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.cluster' with 'bedtool.BedTool.cluster'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.complement' with 'bedtool.BedTool.complement'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.subtract' with 'bedtool.BedTool.subtract'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.slop' with 'bedtool.BedTool.slop'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.flank' with 'bedtool.BedTool.flank'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sort' with 'bedtool.BedTool.sort'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random' with 'bedtool.BedTool.random'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.shuffle' with 'bedtool.BedTool.shuffle'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.annotate' with 'bedtool.BedTool.annotate'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_intersect' with 'bedtool.BedTool.multi_intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.union_bedgraphs' with 'bedtool.BedTool.union_bedgraphs'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_bed' with 'bedtool.BedTool.pair_to_bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.pair_to_pair' with 'bedtool.BedTool.pair_to_pair'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_bed' with 'bedtool.BedTool.bam_to_bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.to_bam' with 'bedtool.BedTool.to_bam'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bedpe_to_bam' with 'bedtool.BedTool.bedpe_to_bam'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bed6' with 'bedtool.BedTool.bed6'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bam_to_fastq' with 'bedtool.BedTool.bam_to_fastq'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.sequence' with 'bedtool.BedTool.sequence'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.mask_fasta' with 'bedtool.BedTool.mask_fasta'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.nucleotide_content' with 'bedtool.BedTool.nucleotide_content'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.multi_bam_coverage' with 'bedtool.BedTool.multi_bam_coverage'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tag_bam' with 'bedtool.BedTool.tag_bam'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.jaccard' with 'bedtool.BedTool.jaccard'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.reldist' with 'bedtool.BedTool.reldist'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.overlap' with 'bedtool.BedTool.overlap'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.links' with 'bedtool.BedTool.links'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.igv' with 'bedtool.BedTool.igv'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.window_maker' with 'bedtool.BedTool.window_maker'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.groupby' with 'bedtool.BedTool.groupby'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.expand' with 'bedtool.BedTool.expand'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.each' with 'bedtool.BedTool.each'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.filter' with 'bedtool.BedTool.filter'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.split' with 'bedtool.BedTool.split'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.truncate_to_chrom' with 'bedtool.BedTool.truncate_to_chrom'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.remove_invalid' with 'bedtool.BedTool.remove_invalid'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.three_prime' with 'featurefuncs.three_prime'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.five_prime' with 'featurefuncs.five_prime'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.TSS' with 'featurefuncs.TSS'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.extend_fields' with 'featurefuncs.extend_fields'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.center' with 'featurefuncs.center'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.midpoint' with 'featurefuncs.midpoint'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.greater_than' with 'featurefuncs.greater_than'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.less_than' with 'featurefuncs.less_than'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.normalized_to_length' with 'featurefuncs.normalized_to_length'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.rename' with 'featurefuncs.rename'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bedgraph_scale' with 'featurefuncs.bedgraph_scale'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.add_color' with 'featurefuncs.add_color'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.gff2bed' with 'featurefuncs.gff2bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.featurefuncs.bed2gff' with 'featurefuncs.bed2gff'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.all_hits' with 'bedtool.BedTool.all_hits'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. 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[autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count' with 'bedtool.BedTool.count'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.field_count' with 'bedtool.BedTool.field_count'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.file_type' with 'bedtool.BedTool.file_type'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.parallel_apply' with 'bedtool.BedTool.parallel_apply'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomstats' with 'bedtool.BedTool.randomstats'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. 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[autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.save_seqs' with 'bedtool.BedTool.save_seqs'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.seq' with 'bedtool.BedTool.seq'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.liftover' with 'bedtool.BedTool.liftover'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.colormap_normalize' with 'bedtool.BedTool.colormap_normalize'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.relative_distance' with 'bedtool.BedTool.relative_distance'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.example_bedtool' with 'bedtool.example_bedtool'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.list_example_files' with 'filenames.list_example_files'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.filenames.example_filename' with 'filenames.example_filename'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.Interval' with 'cbedtools.Interval'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.cbedtools.create_interval_from_list' with 'cbedtools.create_interval_from_list'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_bedtools_path' with 'helpers.set_bedtools_path'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_tempdir' with 'helpers.get_tempdir'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.set_tempdir' with 'helpers.set_tempdir'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.cleanup' with 'helpers.cleanup'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.debug_mode' with 'debug_mode'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.get_chromsizes_from_ucsc' with 'helpers.get_chromsizes_from_ucsc'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes' with 'helpers.chromsizes'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.helpers.chromsizes_to_file' with 'helpers.chromsizes_to_file'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.parallel.parallel_apply' with 'parallel.parallel_apply'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.Track' with 'contrib.plotting.Track'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.TrackCollection' with 'contrib.plotting.TrackCollection'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_heatmap' with 'contrib.plotting.binary_heatmap'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.binary_summary' with 'contrib.plotting.binary_summary'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.BedToolsDemo' with 'contrib.plotting.BedToolsDemo'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.plotting.ConfiguredBedToolsDemo' with 'contrib.plotting.ConfiguredBedToolsDemo'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bam_to_bigwig' with 'contrib.bigwig.bam_to_bigwig'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.bedgraph_to_bigwig' with 'contrib.bigwig.bedgraph_to_bigwig'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigwig.wig_to_bigwig' with 'contrib.bigwig.wig_to_bigwig'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed' with 'contrib.bigbed.bigbed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.bigbed.bigbed_to_bed' with 'contrib.bigbed.bigbed_to_bed'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.IntersectionMatrix' with 'contrib.IntersectionMatrix'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker' with 'contrib.venn_maker'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.venn_maker' with 'contrib.venn_maker.venn_maker'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.venn_maker.cleaned_intersect' with 'contrib.venn_maker.cleaned_intersect'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.tag_bedpe' with 'contrib.long_range_interaction.tag_bedpe'. [autosummary.import_cycle] WARNING: Summarised items should not include the current module. Replace 'pybedtools.contrib.long_range_interaction.cis_trans_interactions' with 'contrib.long_range_interaction.cis_trans_interactions'. [autosummary.import_cycle] /build/reproducible-path/python-pybedtools-0.10.0/docs/source/topical-genome.rst:55: ERROR: Unknown target name: "genomepy". [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.normalized_to_length.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.normalized_to_length /build/reproducible-path/python-pybedtools-0.10.0/docs/source/pybedtools.featurefuncs.rename.rst: document is referenced in multiple toctrees: ['autodoc_source', 'autodoc_source'], selecting: autodoc_source <- pybedtools.featurefuncs.rename done preparing documents... done copying assets... copying assets: done running tests... Document: autodocs/pybedtools.bedtool.BedTool.annotate ------------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.cat ------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.complement -------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.count --------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.coverage ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.cut ------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.each -------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.field_count --------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.file_type ------------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.filter ---------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.flank --------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.genome_coverage ------------------------------------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.groupby ----------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.head -------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.mask_fasta -------------------------------------------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.merge --------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.moveto ---------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.overlap ----------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.random ---------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.randomintersection ---------------------------------------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.randomstats --------------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.remove_invalid ------------------------------------------------------------ 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.save_seqs ------------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.saveas ---------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.sequence ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.set_chromsizes ------------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.shuffle ----------------------------------------------------- 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.sort -------------------------------------------------- 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.subtract ------------------------------------------------------ 1 items passed all tests: 4 tests in default 4 tests in 1 items. 4 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.total_coverage ------------------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.bedtool.BedTool.with_attrs -------------------------------------------------------- 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.cbedtools.Interval ------------------------------------------------ 1 items passed all tests: 3 tests in default 3 tests in 1 items. 3 passed and 0 failed. Test passed. Document: autodocs/pybedtools.cbedtools.create_interval_from_list ----------------------------------------------------------------- 1 items passed all tests: 1 tests in default 1 tests in 1 items. 1 passed and 0 failed. Test passed. Document: autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions ----------------------------------------------------------------------------------- ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: iterator, n, extra = tag_bedpe(bedpe, queries) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in iterator, n, extra = tag_bedpe(bedpe, queries) ^^^^^^^^^ NameError: name 'tag_bedpe' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: for (label, group1, group2) in iterator: group1 = sorted(group1, key=lambda x: str(x)) group2 = sorted(group2, key=lambda x: str(x)) for i in group1: print(i, end='') # doctest: +NORMALIZE_WHITESPACE for i in group2: print(i, end='') # doctest: +NORMALIZE_WHITESPACE Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in for (label, group1, group2) in iterator: ^^^^^^^^ NameError: name 'iterator' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks}) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks}) ^^^^^^^^^ NameError: name 'tag_bedpe' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: df = cis_trans_interactions(iterator, n, extra) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in df = cis_trans_interactions(iterator, n, extra) ^^^^^^^^^^^^^^^^^^^^^^ NameError: name 'cis_trans_interactions' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: print(df.sort_values(list(df.columns)).reset_index(drop=True)) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in print(df.sort_values(list(df.columns)).reset_index(drop=True)) ^^ NameError: name 'df' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: print((df[df.target_label == 'tss']).sort_values(list(df.columns)).reset_index(drop=True)) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in print((df[df.target_label == 'tss']).sort_values(list(df.columns)).reset_index(drop=True)) ^^ NameError: name 'df' is not defined ********************************************************************** File "../../pybedtools/contrib/long_range_interaction.py", line ?, in default Failed example: assert set(df.loc[df.target_name == 'gene2', 'distal_name']).difference('.') == set([u'gene1', u'peak1']) Exception raised: Traceback (most recent call last): File "/usr/lib/python3.12/doctest.py", line 1368, in __run exec(compile(example.source, filename, "single", File "", line 1, in assert set(df.loc[df.target_name == 'gene2', 'distal_name']).difference('.') == set([u'gene1', u'peak1']) ^^ NameError: name 'df' is not defined ********************************************************************** 1 items had failures: 7 of 18 in default 18 tests in 1 items. 11 passed and 7 failed. ***Test Failed*** 7 failures. Document: autodocs/pybedtools.contrib.plotting.Track ---------------------------------------------------- 1 items passed all tests: 7 tests in default 7 tests in 1 items. 7 passed and 0 failed. Test passed. Document: autodocs/pybedtools.filenames.list_example_files ---------------------------------------------------------- 1 items passed all tests: 5 tests in default 5 tests in 1 items. 5 passed and 0 failed. Test passed. Document: autodocs/pybedtools.helpers.chromsizes ------------------------------------------------ 1 items passed all tests: 2 tests in default 2 tests in 1 items. 2 passed and 0 failed. Test passed. Document: autodocs/pybedtools.parallel.parallel_apply ----------------------------------------------------- 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: default-arguments --------------------------- 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: each -------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: filtering ------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: history ----------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: intersections ----------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: intervals ------------------- 1 items passed all tests: 50 tests in default 50 tests in 1 items. 50 passed and 0 failed. Test passed. Document: piping ---------------- 1 items passed all tests: 17 tests in default 17 tests in 1 items. 17 passed and 0 failed. Test passed. Document: save-results ---------------------- 1 items passed all tests: 8 tests in default 8 tests in 1 items. 8 passed and 0 failed. Test passed. Document: topical-bam --------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-create-a-bedtool ---------------------------------- 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-design-principles ----------------------------------- 1 items passed all tests: 15 tests in default 15 tests in 1 items. 15 passed and 0 failed. Test passed. Document: topical-genome ------------------------ 1 items passed all tests: 13 tests in default 13 tests in 1 items. 13 passed and 0 failed. Test passed. Document: topical-iterators --------------------------- 1 items passed all tests: 20 tests in default 20 tests in 1 items. 20 passed and 0 failed. Test passed. Document: topical-low-level-ops ------------------------------- 1 items passed all tests: 6 tests in default 6 tests in 1 items. 6 passed and 0 failed. Test passed. Document: topical-random ------------------------ 1 items passed all tests: 10 tests in default 10 tests in 1 items. 10 passed and 0 failed. Test passed. Document: topical-saving ------------------------ 1 items passed all tests: 14 tests in default 14 tests in 1 items. 14 passed and 0 failed. Test passed. Doctest summary =============== 387 tests 7 failures in tests 0 failures in setup code 0 failures in cleanup code build finished with problems, 126 warnings. make[1]: *** [Makefile:137: doctest] Error 1 make[1]: Leaving directory '/build/reproducible-path/python-pybedtools-0.10.0/docs' E: pybuild pybuild:389: test: plugin distutils failed with: exit code=2: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; make clean doctest dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.13 3.12" returned exit code 13 make: *** [debian/rules:30: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/28056 and its subdirectories Thu Dec 19 03:00:13 UTC 2024 W: No second build log, what happened?