Your message dated Sat, 17 Oct 2026 18:54:15 +0000
with message-id <[email protected]>
and subject line Bug#1149833: fixed in python-pybedtools 0.12.1-2
has caused the Debian Bug report #1149833,
regarding python-pybedtools: autopkgtest regression
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.
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--
1149833: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1149833
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-pybedtools
Version: 0.12.1-1
Severity: serious
https://tracker.debian.org/pkg/python-pybedtools
Migration status for python-pybedtools (0.10.0-6 to 0.12.1-1): BLOCKED:
Rejected/violates migration policy/introduces a regression
Issues preventing migration:
∙ ∙ Autopkgtest for python-pybedtools/0.12.1-1: amd64: Regression ♻ (reference
♻), arm64: Regression ♻ (reference ♻), armhf: Regression ♻ (reference ♻), i386:
Regression ♻ (reference ♻), ppc64el: Regression ♻ (reference ♻)
...
117s =================================== FAILURES
===================================
117s ________________________________ test_tabix_csi
________________________________
117s
117s def test_tabix_csi():
117s for idx_type in ("tbi", "csi"):
117s try:
117s a = pybedtools.example_bedtool("a.bed")
117s > t = a.tabix(force=True, use_csi=True if idx_type == "csi"
else False)
117s
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s
117s /usr/lib/python3/dist-packages/pybedtools/test/test_1.py:135:
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _
117s /usr/lib/python3/dist-packages/pybedtools/bedtool.py:845: in tabix
117s fn = self.bgzip(in_place=in_place, force=force, is_sorted=is_sorted)
117s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s /usr/lib/python3/dist-packages/pybedtools/bedtool.py:908: in bgzip
117s pysam.tabix_compress(fn, outfn, force=force)
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _
117s
117s > ???
117s E OSError: could not open
'/usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz' for writing
117s
117s pysam/libctabix.pyx:843: OSError
117s
117s During handling of the above exception, another exception occurred:
117s
117s def test_tabix_csi():
117s for idx_type in ("tbi", "csi"):
117s try:
117s a = pybedtools.example_bedtool("a.bed")
117s t = a.tabix(force=True, use_csi=True if idx_type == "csi"
else False)
117s assert t._tabixed()
117s results = t.tabix_intervals("chr1:99-200")
117s results = str(results)
117s print(results)
117s assert results == fix(
117s """
117s chr1 1 100 feature1 0 +
117s chr1 100 200 feature2 0 +
117s chr1 150 500 feature3 0 -"""
117s )
117s
117s assert str(t.tabix_intervals(a[2])) == fix(
117s """
117s chr1 100 200 feature2 0 +
117s chr1 150 500 feature3 0 -"""
117s )
117s
117s finally:
117s # clean up
117s fns = [
117s pybedtools.example_filename("a.bed.gz"),
117s > pybedtools.example_filename("a.bed.gz." + idx_type),
117s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s ]
117s
117s /usr/lib/python3/dist-packages/pybedtools/test/test_1.py:157:
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _
117s
117s fn = '/usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz.tbi'
117s
117s def example_filename(fn):
117s """
117s Return a bed file from the pybedtools examples directory. Use
117s func:`list_example_files` to see a list of files that are included.
117s """
117s fn = os.path.join(data_dir(), fn)
117s if not os.path.exists(fn):
117s msg = "%s does not exist" % fn
117s > raise FileNotFoundError(msg)
117s E FileNotFoundError:
/usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz.tbi does not exist
117s
117s /usr/lib/python3/dist-packages/pybedtools/filenames.py:26:
FileNotFoundError
117s ____________________________ test_tabix_contigs_csi
____________________________
117s
117s def test_tabix_contigs_csi():
117s a = pybedtools.example_bedtool("a.bed")
117s > a = a.tabix(force=True, use_csi=True)
117s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s
117s /usr/lib/python3/dist-packages/pybedtools/test/test_1.py:197:
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _
117s /usr/lib/python3/dist-packages/pybedtools/bedtool.py:845: in tabix
117s fn = self.bgzip(in_place=in_place, force=force, is_sorted=is_sorted)
117s ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
117s /usr/lib/python3/dist-packages/pybedtools/bedtool.py:908: in bgzip
117s pysam.tabix_compress(fn, outfn, force=force)
117s _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
_ _ _
117s
117s > ???
117s E OSError: could not open
'/usr/lib/python3/dist-packages/pybedtools/test/data/a.bed.gz' for writing
117s
117s pysam/libctabix.pyx:843: OSError
117s =========================== short test summary info
============================
117s FAILED test/test_1.py::test_tabix_csi - FileNotFoundError:
/usr/lib/python3/d...
117s FAILED test/test_1.py::test_tabix_contigs_csi - OSError: could not open
'/usr...
117s =========== 2 failed, 507 passed, 2 deselected, 3 xfailed in 10.74s
============
118s E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1:
cd /tmp/autopkgtest.2PZ4Fh/autopkgtest_tmp/build; python3.14 -m pytest -k "not
test_chromsizes" --pyargs pybedtools
118s pybuild-autopkgtest: error: pybuild --autopkgtest --test-pytest -i
python{version} -p 3.14 --parallel= returned exit code 13
118s make: *** [/tmp/zZm58GjnHe/run:4: pybuild-autopkgtest] Error 25
118s pybuild-autopkgtest: error: /tmp/zZm58GjnHe/run pybuild-autopkgtest
returned exit code 2
118s autopkgtest [08:54:10]: test pybuild-autopkgtest: -----------------------]
118s autopkgtest [08:54:10]: test pybuild-autopkgtest: - - - - - - - - - -
results - - - - - - - - - -
118s pybuild-autopkgtest FAIL non-zero exit status 25
...
--- End Message ---
--- Begin Message ---
Source: python-pybedtools
Source-Version: 0.12.1-2
Done: Étienne Mollier <[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.
Étienne Mollier <[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: Sat, 17 Oct 2026 19:28:36 +0200
Source: python-pybedtools
Architecture: source
Version: 0.12.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1149833
Changes:
python-pybedtools (0.12.1-2) unstable; urgency=medium
.
* Team upload.
* skip-tests-in-autopkgtest-context.patch: new.
Skip some tests in autopkgtest context, because otherwise they attempt
to write into the test data directory provided by the package, which
is read-only. (Closes: #1149833)
* d/copyright: remove the unused paragraph about plain GPL-2.
* d/control: provide an extended description to python-pybedtools-doc.
* fix-privacy-breaches.patch: new: remove linked images.
* d/python3-pybedtools.lintian-overrides: flag false positives.
* define_filenotfounderror_python2.patch: normalise the timestamp.
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