Your message dated Mon, 06 Oct 2025 18:20:15 +0000
with message-id <[email protected]>
and subject line Bug#1116873: fixed in python-pybedtools 0.10.0-5
has caused the Debian Bug report #1116873,
regarding python-pybedtools: FTBFS with the nocheck build profile
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1116873: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1116873
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:python-pybedtools
Version: 0.10.0-4
Severity: important
Tags: forky sid ftbfs
User: [email protected]
Usertags: ftbfs-nocheck-profile
Dear maintainer:
During a rebuild of all packages in unstable using the nocheck build profile,
your package failed to build.
Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202509/
A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:
https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck
(It's a wiki, so you are welcome to contribute)
[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:python-pybedtools, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3,sphinxdoc --buildsystem=pybuild
debian/rules override_dh_auto_clean
[... snipped ...]
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/mpl-expected.png ->
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/test_1.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/snps.bed.gz ->
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/gdc.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/d.gff ->
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/test.fa.fai ->
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/hg19.gff ->
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/small.fastq ->
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/venn.b.bed ->
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/gdc.sorted.bam.bai ->
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/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.bam ->
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/issue319.vcf.gz
-> 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/exons.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/example.narrowPeak ->
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.gff ->
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/tag_test1.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/multibamcov_test.bed ->
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/test_tsses.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/gdc.othersort.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/c.gff ->
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/genome.fa ->
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/1000genomes-example.vcf
-> 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/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/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/a.igv_script ->
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/vcf-stderr-test.bed ->
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/vcf-stderr-test.vcf ->
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/x.bam ->
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/b.bed ->
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/hg38-problem.bed ->
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/mm9.bed12 ->
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/issue_121.bam
-> 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/x.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/a.bed ->
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/expand_test.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/v.vcf ->
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/BEAF_Kc_Bushey_2009.bed
-> build/bdist.linux-x86_64/wheel/./pybedtools/test/data
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_cases.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_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/paths.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/stats.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
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/bedtool.py ->
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.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/bedFile.cpp ->
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/gzstream.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/fileType.h ->
build/bdist.linux-x86_64/wheel/./pybedtools/include
copying build/lib.linux-x86_64-cpython-313/pybedtools/cbedtools.pxd ->
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
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/.tmp-_ksl_9ri/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'
adding 'pybedtools/cbedtools.cpython-313-x86_64-linux-gnu.so'
adding 'pybedtools/cbedtools.pxd'
adding 'pybedtools/cbedtools.pyx'
adding 'pybedtools/featurefuncs.cpython-313-x86_64-linux-gnu.so'
adding 'pybedtools/featurefuncs.pyx'
adding 'pybedtools/filenames.py'
adding 'pybedtools/genome_registry.py'
adding 'pybedtools/helpers.py'
adding 'pybedtools/logger.py'
adding 'pybedtools/parallel.py'
adding 'pybedtools/paths.py'
adding 'pybedtools/settings.py'
adding 'pybedtools/stats.py'
adding 'pybedtools/version.py'
adding 'pybedtools/contrib/__init__.py'
adding 'pybedtools/contrib/bigbed.py'
adding 'pybedtools/contrib/bigwig.py'
adding 'pybedtools/contrib/intersection_matrix.py'
adding 'pybedtools/contrib/long_range_interaction.py'
adding 'pybedtools/contrib/plotting.py'
adding 'pybedtools/contrib/venn_maker.py'
adding 'pybedtools/include/bedFile.cpp'
adding 'pybedtools/include/bedFile.h'
adding 'pybedtools/include/fileType.cpp'
adding 'pybedtools/include/fileType.h'
adding 'pybedtools/include/gzstream.cpp'
adding 'pybedtools/include/gzstream.h'
adding 'pybedtools/include/lineFileUtilities.h'
adding 'pybedtools/test/__init__.py'
adding 'pybedtools/test/gchart-expected.png'
adding 'pybedtools/test/genomepy_integration.py'
adding 'pybedtools/test/mpl-expected.png'
adding 'pybedtools/test/prevent_open_file_regression'
adding 'pybedtools/test/regression_tests.py'
adding 'pybedtools/test/test_1.py'
adding 'pybedtools/test/test_cases.yaml'
adding 'pybedtools/test/test_cbedtools.py'
adding 'pybedtools/test/test_contrib.py'
adding 'pybedtools/test/test_gzip_support.py'
adding 'pybedtools/test/test_helpers.py'
adding 'pybedtools/test/test_issues.py'
adding 'pybedtools/test/test_iter.py'
adding 'pybedtools/test/test_len_leak.py'
adding 'pybedtools/test/test_merge215.yaml'
adding 'pybedtools/test/test_merge227.yaml'
adding 'pybedtools/test/test_pathlib.py'
adding 'pybedtools/test/test_shuffle215.yaml'
adding 'pybedtools/test/test_shuffle227.yaml'
adding 'pybedtools/test/tfuncs.py'
adding 'pybedtools/test/data/1000genomes-example.vcf'
adding 'pybedtools/test/data/164.gtf'
adding 'pybedtools/test/data/BEAF_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/CTCF_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/Cp190_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/SuHw_Kc_Bushey_2009.bed'
adding 'pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed'
adding 'pybedtools/test/data/__init__.py'
adding 'pybedtools/test/data/a.bed'
adding 'pybedtools/test/data/a.igv_script'
adding 'pybedtools/test/data/a.links.html'
adding 'pybedtools/test/data/b.bed'
adding 'pybedtools/test/data/bedpe.bed'
adding 'pybedtools/test/data/bedpe2.bed'
adding 'pybedtools/test/data/c.gff'
adding 'pybedtools/test/data/d.gff'
adding 'pybedtools/test/data/democonfig.yaml'
adding 'pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz'
adding 'pybedtools/test/data/dm3-chr2L-5M.gff.gz'
adding 'pybedtools/test/data/example.narrowPeak'
adding 'pybedtools/test/data/exons.gff'
adding 'pybedtools/test/data/expand_test.bed'
adding 'pybedtools/test/data/gdc.1.100.bam'
adding 'pybedtools/test/data/gdc.1.100.bam.bai'
adding 'pybedtools/test/data/gdc.50.200.bam'
adding 'pybedtools/test/data/gdc.50.200.bam.bai'
adding 'pybedtools/test/data/gdc.bam'
adding 'pybedtools/test/data/gdc.bed'
adding 'pybedtools/test/data/gdc.cram'
adding 'pybedtools/test/data/gdc.gff'
adding 'pybedtools/test/data/gdc.gff.gz'
adding 'pybedtools/test/data/gdc.othersort.bam'
adding 'pybedtools/test/data/gdc.sorted.bam'
adding 'pybedtools/test/data/gdc.sorted.bam.bai'
adding 'pybedtools/test/data/genome.fa'
adding 'pybedtools/test/data/hg19.gff'
adding 'pybedtools/test/data/hg38-base.bed'
adding 'pybedtools/test/data/hg38-problem.bed'
adding 'pybedtools/test/data/issue319.bed'
adding 'pybedtools/test/data/issue319.out.bed'
adding 'pybedtools/test/data/issue319.vcf.gz'
adding 'pybedtools/test/data/issue_121.bam'
adding 'pybedtools/test/data/m1.bed'
adding 'pybedtools/test/data/mm9.bed12'
adding 'pybedtools/test/data/multibamcov_test.bed'
adding 'pybedtools/test/data/reads.bam'
adding 'pybedtools/test/data/rmsk.hg18.chr21.small.bed'
adding 'pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz'
adding 'pybedtools/test/data/small.bam'
adding 'pybedtools/test/data/small.fastq'
adding 'pybedtools/test/data/snps.bed.gz'
adding 'pybedtools/test/data/tag_test1.bed'
adding 'pybedtools/test/data/tag_test2.bed'
adding 'pybedtools/test/data/test.fa'
adding 'pybedtools/test/data/test.fa.fai'
adding 'pybedtools/test/data/test_bedpe.bed'
adding 'pybedtools/test/data/test_peaks.bed'
adding 'pybedtools/test/data/test_tsses.bed'
adding 'pybedtools/test/data/v.vcf'
adding 'pybedtools/test/data/vcf-stderr-test.bed'
adding 'pybedtools/test/data/vcf-stderr-test.vcf'
adding 'pybedtools/test/data/venn.b.bed'
adding 'pybedtools/test/data/venn.c.bed'
adding 'pybedtools/test/data/x.bam'
adding 'pybedtools/test/data/x.bed'
adding 'pybedtools/test/data/y.bam'
adding 'pybedtools-0.10.0.dist-info/licenses/LICENSE.txt'
adding 'pybedtools-0.10.0.dist-info/METADATA'
adding 'pybedtools-0.10.0.dist-info/WHEEL'
adding 'pybedtools-0.10.0.dist-info/top_level.txt'
adding 'pybedtools-0.10.0.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built pybedtools-0.10.0-cp313-cp313-linux_x86_64.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with
"installer" module
debian/rules execute_after_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd docs ; PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pybedtools/build
python3.13 -m sphinx -N -b html source html
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, 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
Extension error (sphinx.ext.autosummary)!
Versions
========
* Platform: linux;
(Linux-6.12.48+deb13-cloud-amd64-x86_64-with-glibc2.41)
* Python version: 3.13.7 (CPython)
* Sphinx version: 8.2.3
* Docutils version: 0.21.2
* Jinja2 version: 3.1.6
* Pygments version: 2.18.0
Last Messages
=============
None.
Loaded Extensions
=================
None.
Traceback
=========
File "/usr/lib/python3/dist-packages/sphinx/events.py", line 415, in emit
raise ExtensionError(
...<4 lines>...
) from exc
sphinx.errors.ExtensionError: Handler <function process_generate_options at
0x7f3256655620> for event 'builder-inited' threw an exception (exception: no
module named pybedtools.contrib.plotting)
The full traceback has been saved in:
/tmp/sphinx-err-4tc7_5u4.log
To report this error to the developers, please open an issue at
<https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message
can be provided next time.
make[1]: *** [debian/rules:25: execute_after_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:22: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: python-pybedtools
Source-Version: 0.10.0-5
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-pybedtools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Santiago Vila <[email protected]> (supplier of updated python-pybedtools
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 06 Oct 2025 19:30:00 +0200
Source: python-pybedtools
Architecture: source
Version: 0.10.0-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1116873
Changes:
python-pybedtools (0.10.0-5) unstable; urgency=medium
.
* Team upload.
* d/control: Drop <!nocheck> from python3-matplotlib in BD. Closes: #1116873.
* d/copyright: Do not refer to the old postal address of the FSF.
* d/control: Drop "Rules-Requires-Root: no", not needed anymore.
* d/control: Drop "Priority: optional", not needed anymore.
* d/control: Update standards-version.
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