Diff of the two buildlogs: -- --- b1/build.log 2025-11-02 00:01:37.348727030 +0000 +++ b2/build.log 2025-11-02 00:18:34.365547228 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Dec 4 18:21:07 -12 2026 -I: pbuilder-time-stamp: 1796451667 +I: Current time: Sun Nov 2 14:07:24 +14 2025 +I: pbuilder-time-stamp: 1762042044 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -32,53 +32,85 @@ dpkg-source: info: applying test-tempdir I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23309/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2197013/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 2 00:13 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2197013/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2197013/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='cfc6c8d5b8ec43adbaa033c25e4fa7fc' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='23309' - PS1='# ' - PS2='> ' + INVOCATION_ID=a9005396d0fb4ee4b84bded9e293c890 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2197013 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.06G6fugO/pbuilderrc_zSou --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.06G6fugO/b1 --logfile b1/build.log python-pybedtools_0.10.0-5.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.06G6fugO/pbuilderrc_ND4E --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.06G6fugO/b2 --logfile b2/build.log python-pybedtools_0.10.0-5.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/23309/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2197013/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -91,7 +123,7 @@ Depends: debhelper-compat (= 13), dh-sequence-python3, pybuild-plugin-pyproject, bedtools, cython3, python3-all-dev, python3-setuptools, python3-pysam, python3-matplotlib, python3-pytest, python3-numpy, python3-numpydoc, python3-pandas, python3-psutil, python3-yaml, 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 ... 19869 files and directories currently installed.) +(Reading database ... 19862 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: @@ -393,10 +425,10 @@ Get: 243 http://deb.debian.org/debian forky/main amd64 unzip amd64 6.0-29 [173 kB] Get: 244 http://deb.debian.org/debian forky/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 245 http://deb.debian.org/debian forky/main amd64 r-base-core amd64 4.5.1-1 [28.7 MB] -Fetched 192 MB in 11s (16.8 MB/s) +Fetched 192 MB in 28s (6840 kB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. -(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19869 files and directories currently installed.) +(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 ... 19862 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. @@ -409,7 +441,7 @@ Setting up libexpat1:amd64 (2.7.3-1) ... Setting up python3.13-minimal (3.13.9-1) ... 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 ... 20203 files and directories currently installed.) +(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 ... 20196 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... Selecting previously unselected package media-types. @@ -445,7 +477,7 @@ Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... 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 ... 21218 files and directories currently installed.) +(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 ... 21211 files and directories currently installed.) Preparing to unpack .../000-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package python3-numpy-dev:amd64. @@ -1195,8 +1227,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Dec 5 06:22:06 UTC 2026. -Universal Time is now: Sat Dec 5 06:22:06 UTC 2026. +Local time is now: Sun Nov 2 00:16:38 UTC 2025. +Universal Time is now: Sun Nov 2 00:16:38 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (16.0.0-1) ... @@ -1427,7 +1459,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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_0.10.0-5_source.changes +I: user script /srv/workspace/pbuilder/2197013/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2197013/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/python-pybedtools-0.10.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../python-pybedtools_0.10.0-5_source.changes dpkg-buildpackage: info: source package python-pybedtools dpkg-buildpackage: info: source version 0.10.0-5 dpkg-buildpackage: info: source distribution unstable @@ -1501,39 +1537,39 @@ running build running build_py creating build/lib.linux-x86_64-cpython-313/pybedtools +copying pybedtools/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools +copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-313/pybedtools copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-cpython-313/pybedtools +copying pybedtools/parallel.py -> build/lib.linux-x86_64-cpython-313/pybedtools +copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-313/pybedtools +copying pybedtools/paths.py -> build/lib.linux-x86_64-cpython-313/pybedtools copying pybedtools/version.py -> build/lib.linux-x86_64-cpython-313/pybedtools copying pybedtools/logger.py -> build/lib.linux-x86_64-cpython-313/pybedtools -copying pybedtools/filenames.py -> build/lib.linux-x86_64-cpython-313/pybedtools -copying pybedtools/parallel.py -> build/lib.linux-x86_64-cpython-313/pybedtools -copying pybedtools/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools -copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-313/pybedtools copying pybedtools/helpers.py -> build/lib.linux-x86_64-cpython-313/pybedtools -copying pybedtools/stats.py -> build/lib.linux-x86_64-cpython-313/pybedtools -copying pybedtools/paths.py -> build/lib.linux-x86_64-cpython-313/pybedtools +copying pybedtools/settings.py -> build/lib.linux-x86_64-cpython-313/pybedtools copying pybedtools/bedtool.py -> build/lib.linux-x86_64-cpython-313/pybedtools creating build/lib.linux-x86_64-cpython-313/pybedtools/test -copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test -copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test -copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test -copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test -copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test -copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test -copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test +copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test +copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test copying pybedtools/test/test_1.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test +copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test +copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test +copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test +copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test +copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test copying pybedtools/test/test_pathlib.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test -copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test +copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test copying pybedtools/test/test_issues.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test creating build/lib.linux-x86_64-cpython-313/pybedtools/contrib -copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib -copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib -copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib +copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib +copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib +copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib +copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib -copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools/contrib creating build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data running egg_info @@ -1603,74 +1639,74 @@ copying pybedtools/include/gzstream.cpp -> build/lib.linux-x86_64-cpython-313/pybedtools/include copying pybedtools/include/gzstream.h -> build/lib.linux-x86_64-cpython-313/pybedtools/include copying pybedtools/include/lineFileUtilities.h -> build/lib.linux-x86_64-cpython-313/pybedtools/include -copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/genome.fa -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/genome.fa -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/issue319.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data -copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data +copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-x86_64-cpython-313/pybedtools/test/data copying pybedtools/test/gchart-expected.png -> build/lib.linux-x86_64-cpython-313/pybedtools/test copying pybedtools/test/mpl-expected.png -> build/lib.linux-x86_64-cpython-313/pybedtools/test copying pybedtools/test/prevent_open_file_regression -> build/lib.linux-x86_64-cpython-313/pybedtools/test @@ -1708,136 +1744,136 @@ running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/stats.py -> build/bdist.linux-x86_64/wheel/./pybedtools copying build/lib.linux-x86_64-cpython-313/pybedtools/genome_registry.py -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/version.py -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/logger.py -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/featurefuncs.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pybedtools creating build/bdist.linux-x86_64/wheel/pybedtools/include -copying build/lib.linux-x86_64-cpython-313/pybedtools/include/bedFile.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include -copying build/lib.linux-x86_64-cpython-313/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include copying build/lib.linux-x86_64-cpython-313/pybedtools/include/gzstream.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include copying build/lib.linux-x86_64-cpython-313/pybedtools/include/fileType.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include -copying build/lib.linux-x86_64-cpython-313/pybedtools/include/fileType.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include -copying build/lib.linux-x86_64-cpython-313/pybedtools/include/gzstream.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include copying build/lib.linux-x86_64-cpython-313/pybedtools/include/bedFile.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include -copying build/lib.linux-x86_64-cpython-313/pybedtools/featurefuncs.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/include/gzstream.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include +copying build/lib.linux-x86_64-cpython-313/pybedtools/include/fileType.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include +copying build/lib.linux-x86_64-cpython-313/pybedtools/include/lineFileUtilities.h -> build/bdist.linux-x86_64/wheel/./pybedtools/include +copying build/lib.linux-x86_64-cpython-313/pybedtools/include/bedFile.cpp -> build/bdist.linux-x86_64/wheel/./pybedtools/include +copying build/lib.linux-x86_64-cpython-313/pybedtools/parallel.py -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/filenames.py -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/paths.py -> build/bdist.linux-x86_64/wheel/./pybedtools creating build/bdist.linux-x86_64/wheel/pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/tfuncs.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_cbedtools.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/genomepy_integration.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_1.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_len_leak.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_contrib.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/regression_tests.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/mpl-expected.png -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_gzip_support.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/gchart-expected.png -> build/bdist.linux-x86_64/wheel/./pybedtools/test copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_shuffle227.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_cases.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/tfuncs.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_merge215.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_len_leak.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/gchart-expected.png -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_merge227.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_cbedtools.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test creating build/bdist.linux-x86_64/wheel/pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/b.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/d.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test.fa.fai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/hg38-base.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue_121.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test.fa -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/m1.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/bedpe.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test.fa.fai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/hg19.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/vcf-stderr-test.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/164.gtf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/venn.b.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/a.links.html -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/small.fastq -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.50.200.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/exons.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.1.100.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.cram -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/a.igv_script -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue319.out.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/a.links.html -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/small.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/venn.c.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/genome.fa -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue_121.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.cram -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/multibamcov_test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/exons.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/y.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/small.fastq -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/small.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/hg38-problem.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/c.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/venn.b.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/reads.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.sorted.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/v.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/x.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/1000genomes-example.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/b.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/y.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test_bedpe.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.50.200.bam.bai -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/mm9.bed12 -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/snps.bed.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/hg19.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test_peaks.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.sorted.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/expand_test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue319.vcf.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/genome.fa -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/issue319.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/a.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/democonfig.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/d.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.1.100.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/m1.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/x.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/v.vcf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/tag_test1.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/vcf-stderr-test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/test_tsses.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_iter.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/mpl-expected.png -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_gzip_support.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_shuffle215.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/regression_tests.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_1.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/164.gtf -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/bedpe2.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/a.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/bedpe.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/expand_test.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.othersort.bam -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/tag_test2.bed -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/gdc.gff -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/data/example.narrowPeak -> build/bdist.linux-x86_64/wheel/./pybedtools/test/data copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_pathlib.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_merge227.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_helpers.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_cases.yaml -> build/bdist.linux-x86_64/wheel/./pybedtools/test -copying build/lib.linux-x86_64-cpython-313/pybedtools/test/genomepy_integration.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_iter.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test copying build/lib.linux-x86_64-cpython-313/pybedtools/test/test_issues.py -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/test/prevent_open_file_regression -> build/bdist.linux-x86_64/wheel/./pybedtools/test +copying build/lib.linux-x86_64-cpython-313/pybedtools/featurefuncs.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/version.py -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/logger.py -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pybedtools copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.pxd -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/filenames.py -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/parallel.py -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/featurefuncs.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/helpers.py -> build/bdist.linux-x86_64/wheel/./pybedtools copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pybedtools copying build/lib.linux-x86_64-cpython-313/pybedtools/settings.py -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/helpers.py -> build/bdist.linux-x86_64/wheel/./pybedtools +copying build/lib.linux-x86_64-cpython-313/pybedtools/bedtool.py -> build/bdist.linux-x86_64/wheel/./pybedtools copying build/lib.linux-x86_64-cpython-313/pybedtools/_Window.pyx -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/stats.py -> build/bdist.linux-x86_64/wheel/./pybedtools -copying build/lib.linux-x86_64-cpython-313/pybedtools/paths.py -> build/bdist.linux-x86_64/wheel/./pybedtools creating build/bdist.linux-x86_64/wheel/pybedtools/contrib -copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib -copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/bigbed.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib -copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/bigwig.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib +copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib +copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/long_range_interaction.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/venn_maker.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib +copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/bigbed.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib +copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/intersection_matrix.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/plotting.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib -copying build/lib.linux-x86_64-cpython-313/pybedtools/contrib/__init__.py -> build/bdist.linux-x86_64/wheel/./pybedtools/contrib -copying build/lib.linux-x86_64-cpython-313/pybedtools/bedtool.py -> build/bdist.linux-x86_64/wheel/./pybedtools running install_egg_info Copying pybedtools.egg-info to build/bdist.linux-x86_64/wheel/./pybedtools-0.10.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/pybedtools-0.10.0.dist-info/WHEEL -creating '/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/.tmp-nja26vqs/pybedtools-0.10.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it +creating '/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/.tmp-u2flm0ft/pybedtools-0.10.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'pybedtools/_Window.pyx' adding 'pybedtools/__init__.py' adding 'pybedtools/bedtool.py' @@ -1975,8 +2011,8 @@ 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 -mkdir -p failed for path /nonexistent/first-build/.cache/matplotlib: [Errno 13] Permission denied: '/nonexistent' -Matplotlib created a temporary cache directory at /tmp/matplotlib-v0oboixw because there was an issue with the default path (/nonexistent/first-build/.cache/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. +mkdir -p failed for path /nonexistent/second-build/.cache/matplotlib: [Errno 13] Permission denied: '/nonexistent' +Matplotlib created a temporary cache directory at /tmp/matplotlib-w_vo2k5r because there was an issue with the default path (/nonexistent/second-build/.cache/matplotlib); it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing. [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... @@ -2287,9 +2323,9 @@ preparing documents... done copying assets... copying static files... -Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/basic.css +Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/python-pybedtools-0.10.0/docs/html/_static/alabaster.css copying static files: done copying extra files... @@ -2482,791 +2518,7 @@ The HTML pages are in 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/ ; -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" --pyargs pybedtools -============================= test session starts ============================== -platform linux -- Python 3.13.9, pytest-8.4.2, pluggy-1.6.0 -rootdir: /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build -configfile: pyproject.toml -plugins: typeguard-4.4.4 -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 13.46s ================= -I: pybuild pybuild:334: cd /build/reproducible-path/python-pybedtools-0.10.0/docs ; PYTHONPATH=/build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build python3.13 -m sphinx -b doctest -d build/doctrees source build/doctest -Running Sphinx v8.2.3 -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, autodocs/pybedtools.bedtool.BedTool.absolute_distance.rst, autodocs/pybedtools.bedtool.BedTool.all_hits.rst, autodocs/pybedtools.bedtool.BedTool.annotate.rst, autodocs/pybedtools.bedtool.BedTool.any_hits.rst, autodocs/pybedtools.bedtool.BedTool.as_intervalfile.rst, autodocs/pybedtools.bedtool.BedTool.at.rst, autodocs/pybedtools.bedtool.BedTool.bam_to_bed.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 -building [mo]: targets for 0 po files that are out of date -writing output... -building [doctest]: targets for 157 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:420: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/bedtool.py. - self[section] = content -/usr/lib/python3/dist-packages/numpydoc/docscrape.py:420: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/long_range_interaction.py. - self[section] = content -reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool -/usr/lib/python3/dist-packages/numpydoc/docscrape.py:420: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/bedtool.py. - self[section] = content -reading sources... [ 3%] autodocs/pybedtools.bedtool.BedTool.absolute_distance -reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.all_hits -reading sources... [ 4%] autodocs/pybedtools.bedtool.BedTool.annotate -reading sources... [ 5%] autodocs/pybedtools.bedtool.BedTool.any_hits -reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.as_intervalfile -reading sources... [ 6%] autodocs/pybedtools.bedtool.BedTool.at -reading sources... [ 7%] autodocs/pybedtools.bedtool.BedTool.bam_to_bed -reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bam_to_fastq -reading sources... [ 8%] autodocs/pybedtools.bedtool.BedTool.bed6 -reading sources... [ 9%] autodocs/pybedtools.bedtool.BedTool.bedpe_to_bam -reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.bgzip -reading sources... [ 10%] autodocs/pybedtools.bedtool.BedTool.cat -reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.closest -reading sources... [ 11%] autodocs/pybedtools.bedtool.BedTool.cluster -reading sources... [ 12%] autodocs/pybedtools.bedtool.BedTool.colormap_normalize -reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.complement -reading sources... [ 13%] autodocs/pybedtools.bedtool.BedTool.count -reading sources... [ 14%] autodocs/pybedtools.bedtool.BedTool.count_hits -reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.coverage -reading sources... [ 15%] autodocs/pybedtools.bedtool.BedTool.cut -reading sources... [ 16%] autodocs/pybedtools.bedtool.BedTool.each -reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.expand -reading sources... [ 17%] autodocs/pybedtools.bedtool.BedTool.field_count -reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.file_type -reading sources... [ 18%] autodocs/pybedtools.bedtool.BedTool.filter -reading sources... [ 19%] autodocs/pybedtools.bedtool.BedTool.flank -reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.genome_coverage -reading sources... [ 20%] autodocs/pybedtools.bedtool.BedTool.groupby -reading sources... [ 21%] autodocs/pybedtools.bedtool.BedTool.head -reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.igv -reading sources... [ 22%] autodocs/pybedtools.bedtool.BedTool.intersect -reading sources... [ 23%] autodocs/pybedtools.bedtool.BedTool.introns -reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.jaccard -reading sources... [ 24%] autodocs/pybedtools.bedtool.BedTool.liftover -reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.links -reading sources... [ 25%] autodocs/pybedtools.bedtool.BedTool.map -reading sources... [ 26%] autodocs/pybedtools.bedtool.BedTool.mask_fasta -reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.merge -reading sources... [ 27%] autodocs/pybedtools.bedtool.BedTool.moveto -reading sources... [ 28%] autodocs/pybedtools.bedtool.BedTool.multi_bam_coverage -reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.multi_intersect -reading sources... [ 29%] autodocs/pybedtools.bedtool.BedTool.nucleotide_content -reading sources... [ 30%] autodocs/pybedtools.bedtool.BedTool.overlap -reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_bed -reading sources... [ 31%] autodocs/pybedtools.bedtool.BedTool.pair_to_pair -reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.parallel_apply -reading sources... [ 32%] autodocs/pybedtools.bedtool.BedTool.print_sequence -reading sources... [ 33%] autodocs/pybedtools.bedtool.BedTool.random -reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_jaccard -reading sources... [ 34%] autodocs/pybedtools.bedtool.BedTool.random_op -reading sources... [ 35%] autodocs/pybedtools.bedtool.BedTool.random_subset -/usr/lib/python3/dist-packages/numpydoc/docscrape.py:420: UserWarning: Unknown section Example in the docstring of decorated in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/bedtool.py. - self[section] = content -reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection -reading sources... [ 36%] autodocs/pybedtools.bedtool.BedTool.randomintersection_bp -reading sources... [ 37%] autodocs/pybedtools.bedtool.BedTool.randomstats -reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.relative_distance -reading sources... [ 38%] autodocs/pybedtools.bedtool.BedTool.reldist -reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.remove_invalid -reading sources... [ 39%] autodocs/pybedtools.bedtool.BedTool.save_seqs -reading sources... 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[ 48%] autodocs/pybedtools.bedtool.BedTool.total_coverage -reading sources... [ 49%] autodocs/pybedtools.bedtool.BedTool.truncate_to_chrom -reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.union_bedgraphs -reading sources... [ 50%] autodocs/pybedtools.bedtool.BedTool.window -reading sources... [ 51%] autodocs/pybedtools.bedtool.BedTool.window_maker -reading sources... [ 52%] autodocs/pybedtools.bedtool.BedTool.with_attrs -reading sources... [ 52%] autodocs/pybedtools.bedtool.example_bedtool -reading sources... [ 53%] autodocs/pybedtools.cbedtools.Interval -reading sources... [ 54%] autodocs/pybedtools.cbedtools.create_interval_from_list -reading sources... [ 54%] autodocs/pybedtools.contrib.IntersectionMatrix -reading sources... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed -reading sources... [ 55%] autodocs/pybedtools.contrib.bigbed.bigbed_to_bed -reading sources... [ 56%] autodocs/pybedtools.contrib.bigwig.bam_to_bigwig -reading sources... [ 57%] autodocs/pybedtools.contrib.bigwig.bedgraph_to_bigwig -reading sources... [ 57%] autodocs/pybedtools.contrib.bigwig.wig_to_bigwig -reading sources... [ 58%] autodocs/pybedtools.contrib.long_range_interaction.cis_trans_interactions -reading sources... [ 59%] autodocs/pybedtools.contrib.long_range_interaction.tag_bedpe -/usr/lib/python3/dist-packages/numpydoc/docscrape.py:420: UserWarning: Unknown section Example in the docstring of tag_bedpe in /build/reproducible-path/python-pybedtools-0.10.0/.pybuild/cpython3_3.13_pybedtools/build/pybedtools/contrib/long_range_interaction.py. - self[section] = content -reading sources... [ 59%] autodocs/pybedtools.contrib.plotting.BedToolsDemo -reading sources... [ 60%] autodocs/pybedtools.contrib.plotting.ConfiguredBedToolsDemo -reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.Track -reading sources... [ 61%] autodocs/pybedtools.contrib.plotting.TrackCollection -reading sources... 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[ 95%] topical-design-principles -reading sources... [ 96%] topical-documentation-contents -reading sources... [ 96%] topical-genome -reading sources... [ 97%] topical-iterators -reading sources... [ 97%] topical-low-level-ops -reading sources... [ 98%] topical-random -reading sources... [ 99%] topical-saving -reading sources... [ 99%] topical-wrapping -reading sources... [100%] tutorial-contents - -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool' with 'bedtool.BedTool'. [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. 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[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. 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[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. Replace 'pybedtools.bedtool.BedTool.any_hits' with 'bedtool.BedTool.any_hits'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.count_hits' with 'bedtool.BedTool.count_hits'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix_intervals' with 'bedtool.BedTool.tabix_intervals'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.tabix' with 'bedtool.BedTool.tabix'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.bgzip' with 'bedtool.BedTool.bgzip'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.head' with 'bedtool.BedTool.head'. [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. Replace 'pybedtools.bedtool.BedTool.randomintersection' with 'bedtool.BedTool.randomintersection'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.randomintersection_bp' with 'bedtool.BedTool.randomintersection_bp'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_subset' with 'bedtool.BedTool.random_subset'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_jaccard' with 'bedtool.BedTool.random_jaccard'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.random_op' with 'bedtool.BedTool.random_op'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.saveas' with 'bedtool.BedTool.saveas'. [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. Replace 'pybedtools.bedtool.BedTool.total_coverage' with 'bedtool.BedTool.total_coverage'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.with_attrs' with 'bedtool.BedTool.with_attrs'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.as_intervalfile' with 'bedtool.BedTool.as_intervalfile'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.introns' with 'bedtool.BedTool.introns'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.set_chromsizes' with 'bedtool.BedTool.set_chromsizes'. [autosummary.import_cycle] -WARNING: Summarised items should not include the current module. Replace 'pybedtools.bedtool.BedTool.print_sequence' with 'bedtool.BedTool.print_sequence'. [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". - -Did you want to embed a URI or alias? -The embedded reference must be preceded by whitespace. [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 item passed all tests: - 3 tests in default -3 tests in 1 item. -3 passed. -Test passed. - -Document: autodocs/pybedtools.bedtool.BedTool.cat -------------------------------------------------- -1 item passed all tests: - 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20 tests in default -20 tests in 1 item. -20 passed. -Test passed. - -Document: topical-low-level-ops -------------------------------- -1 item passed all tests: - 6 tests in default -6 tests in 1 item. -6 passed. -Test passed. - -Document: topical-random ------------------------- -1 item passed all tests: - 10 tests in default -10 tests in 1 item. -10 passed. -Test passed. - -Document: topical-saving ------------------------- -1 item passed all tests: - 14 tests in default -14 tests in 1 item. -14 passed. -Test passed. - -Doctest summary -=============== - 387 tests - 0 failures in tests - 0 failures in setup code - 0 failures in cleanup code -build succeeded, 126 warnings. - -Testing of doctests in the sources finished, look at the results in build/doctest/output.txt. +dh: command-omitted: The call to "dh_auto_test -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild @@ -3303,8 +2555,8 @@ dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'pybedtools-bin' in '../pybedtools-bin_0.10.0-5_all.deb'. -dpkg-deb: building package 'python3-pybedtools-dbgsym' in '../python3-pybedtools-dbgsym_0.10.0-5_amd64.deb'. dpkg-deb: building package 'python3-pybedtools' in '../python3-pybedtools_0.10.0-5_amd64.deb'. +dpkg-deb: building package 'python3-pybedtools-dbgsym' in '../python3-pybedtools-dbgsym_0.10.0-5_amd64.deb'. dpkg-deb: building package 'python-pybedtools-doc' in '../python-pybedtools-doc_0.10.0-5_all.deb'. dpkg-genbuildinfo --build=binary -O../python-pybedtools_0.10.0-5_amd64.buildinfo dpkg-genchanges --build=binary -O../python-pybedtools_0.10.0-5_amd64.changes @@ -3314,12 +2566,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2197013/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2197013/tmp/hooks/B01_cleanup finished 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/23309 and its subdirectories -I: Current time: Fri Dec 4 18:24:36 -12 2026 -I: pbuilder-time-stamp: 1796451876 +I: removing directory /srv/workspace/pbuilder/2197013 and its subdirectories +I: Current time: Sun Nov 2 14:18:34 +14 2025 +I: pbuilder-time-stamp: 1762042714