Your message dated Sun, 14 Sep 2025 00:08:15 +0000
with message-id <[email protected]>
and subject line Bug#1114298: fixed in python-biopython 1.85+dfsg-5
has caused the Debian Bug report #1114298,
regarding python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i
python{version} -p 3.13 --test --system=custom "--test-args= \\
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.)
--
1114298: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114298
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:python-biopython
Version: 1.85+dfsg-4
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, 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/
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-biopython, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
pybuild --clean -i python{version} -p 3.13
I: pybuild base:311: python3.13 setup.py clean
/usr/lib/python3/dist-packages/setuptools/dist.py:759:
SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of a SPDX
license expression:
License :: Freely Distributable
[... snipped ...]
Bio.PDB.PDBList docstring test ... ok
Bio.PDB.PDBMLParser docstring test ... ok
Bio.PDB.PDBParser docstring test ... ok
Bio.PDB.PICIO docstring test ... ok
Bio.PDB.PSEA docstring test ... ok
Bio.PDB.Polypeptide docstring test ... ok
Bio.PDB.Residue docstring test ... ok
Bio.PDB.ResidueDepth docstring test ... ok
Bio.PDB.SASA docstring test ... ok
Bio.PDB.SCADIO docstring test ... ok
Bio.PDB.Selection docstring test ... ok
Bio.PDB.Structure docstring test ... ok
Bio.PDB.StructureAlignment docstring test ... ok
Bio.PDB.StructureBuilder docstring test ... ok
Bio.PDB.Superimposer docstring test ... ok
Bio.PDB._bcif_helper docstring test ... ok
Bio.PDB.alphafold_db docstring test ... ok
Bio.PDB.binary_cif docstring test ... ok
Bio.PDB.ccealign docstring test ... ok
Bio.PDB.cealign docstring test ... ok
Bio.PDB.ic_data docstring test ... ok
Bio.PDB.ic_rebuild docstring test ... ok
Bio.PDB.internal_coords docstring test ... ok
Bio.PDB.kdtrees docstring test ... ok
Bio.PDB.mmcifio docstring test ... ok
Bio.PDB.mmtf docstring test ... ok
Bio.PDB.mmtf.DefaultParser docstring test ... ok
Bio.PDB.mmtf.mmtfio docstring test ... ok
Bio.PDB.parse_pdb_header docstring test ... ok
Bio.PDB.qcprot docstring test ... ok
Bio.PDB.vectors docstring test ... ok
Bio.Pathway docstring test ... ok
Bio.Pathway.Rep docstring test ... ok
Bio.Pathway.Rep.Graph docstring test ... ok
Bio.Pathway.Rep.MultiGraph docstring test ... ok
Bio.Phylo docstring test ... ok
Bio.Phylo.Applications docstring test ... ok
Bio.Phylo.Applications._Fasttree docstring test ... ok
Bio.Phylo.Applications._Phyml docstring test ... ok
Bio.Phylo.Applications._Raxml docstring test ... ok
Bio.Phylo.BaseTree docstring test ... ok
Bio.Phylo.CDAO docstring test ... ok
Bio.Phylo.CDAOIO docstring test ... ok
Bio.Phylo.Consensus docstring test ... ok
Bio.Phylo.NeXML docstring test ... ok
Bio.Phylo.NeXMLIO docstring test ... ok
Bio.Phylo.Newick docstring test ... ok
Bio.Phylo.NewickIO docstring test ... ok
Bio.Phylo.NexusIO docstring test ... ok
Bio.Phylo.PAML docstring test ... ok
Bio.Phylo.PAML._paml docstring test ... ok
Bio.Phylo.PAML._parse_baseml docstring test ... ok
Bio.Phylo.PAML._parse_codeml docstring test ... ok
Bio.Phylo.PAML._parse_yn00 docstring test ... ok
Bio.Phylo.PAML.baseml docstring test ... ok
Bio.Phylo.PAML.chi2 docstring test ... ok
Bio.Phylo.PAML.codeml docstring test ... ok
Bio.Phylo.PAML.yn00 docstring test ... ok
Bio.Phylo.PhyloXML docstring test ... ok
Bio.Phylo.PhyloXMLIO docstring test ... ok
Bio.Phylo.TreeConstruction docstring test ... ok
Bio.Phylo._cdao_owl docstring test ... ok
Bio.Phylo._io docstring test ... ok
Bio.Phylo._utils docstring test ... ok
Bio.PopGen docstring test ... ok
Bio.PopGen.GenePop docstring test ... ok
Bio.PopGen.GenePop.Controller docstring test ... ok
Bio.PopGen.GenePop.EasyController docstring test ... ok
Bio.PopGen.GenePop.FileParser docstring test ... ok
Bio.PopGen.GenePop.LargeFileParser docstring test ... ok
Bio.Restriction docstring test ... ok
Bio.Restriction.PrintFormat docstring test ... ok
Bio.Restriction.Restriction docstring test ... ok
Bio.Restriction.Restriction_Dictionary docstring test ... ok
Bio.SCOP docstring test ... ok
Bio.SCOP.Cla docstring test ... ok
Bio.SCOP.Des docstring test ... ok
Bio.SCOP.Dom docstring test ... ok
Bio.SCOP.Hie docstring test ... ok
Bio.SCOP.Raf docstring test ... ok
Bio.SCOP.Residues docstring test ... ok
Bio.SVDSuperimposer docstring test ... ok
Bio.SearchIO docstring test ... ok
Bio.SearchIO.BlastIO docstring test ... ok
Bio.SearchIO.BlastIO.blast_tab docstring test ... ok
Bio.SearchIO.BlastIO.blast_xml docstring test ... ok
Bio.SearchIO.BlatIO docstring test ... ok
Bio.SearchIO.ExonerateIO docstring test ... ok
Bio.SearchIO.ExonerateIO._base docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_cigar docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_text docstring test ... ok
Bio.SearchIO.ExonerateIO.exonerate_vulgar docstring test ... ok
Bio.SearchIO.FastaIO docstring test ... ok
Bio.SearchIO.HHsuiteIO docstring test ... ok
Bio.SearchIO.HHsuiteIO.hhsuite2_text docstring test ... ok
Bio.SearchIO.HmmerIO docstring test ... ok
Bio.SearchIO.HmmerIO._base docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer2_text docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_domtab docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_tab docstring test ... ok
Bio.SearchIO.HmmerIO.hmmer3_text docstring test ... ok
Bio.SearchIO.InterproscanIO docstring test ... ok
Bio.SearchIO.InterproscanIO.interproscan_xml docstring test ... ok
Bio.SearchIO._index docstring test ... ok
Bio.SearchIO._model docstring test ... ok
Bio.SearchIO._model._base docstring test ... ok
Bio.SearchIO._model.hit docstring test ... ok
Bio.SearchIO._model.hsp docstring test ... ok
Bio.SearchIO._model.query docstring test ... ok
Bio.SearchIO._utils docstring test ... ok
Bio.Seq docstring test ... ok
Bio.SeqFeature docstring test ... ok
Bio.SeqIO docstring test ... ok
Bio.SeqIO.AbiIO docstring test ... ok
Bio.SeqIO.AceIO docstring test ... ok
Bio.SeqIO.FastaIO docstring test ... ok
Bio.SeqIO.GckIO docstring test ... ok
Bio.SeqIO.GfaIO docstring test ... ok
Bio.SeqIO.IgIO docstring test ... ok
Bio.SeqIO.InsdcIO docstring test ... ok
Bio.SeqIO.Interfaces docstring test ... ok
Bio.SeqIO.NibIO docstring test ... ok
Bio.SeqIO.PdbIO docstring test ... ok
Bio.SeqIO.PhdIO docstring test ... ok
Bio.SeqIO.PirIO docstring test ... ok
Bio.SeqIO.QualityIO docstring test ... ok
Bio.SeqIO.SeqXmlIO docstring test ... ok
Bio.SeqIO.SffIO docstring test ... ok
Bio.SeqIO.SnapGeneIO docstring test ... ok
Bio.SeqIO.SwissIO docstring test ... ok
Bio.SeqIO.TabIO docstring test ... ok
Bio.SeqIO.TwoBitIO docstring test ... ok
Bio.SeqIO.UniprotIO docstring test ... ok
Bio.SeqIO.XdnaIO docstring test ... ok
Bio.SeqIO._index docstring test ... ok
Bio.SeqIO._twoBitIO docstring test ... ok
Bio.SeqRecord docstring test ... ok
Bio.SeqUtils docstring test ... ok
Bio.SeqUtils.CheckSum docstring test ... ok
Bio.SeqUtils.IsoelectricPoint docstring test ... ok
Bio.SeqUtils.MeltingTemp docstring test ... ok
Bio.SeqUtils.ProtParam docstring test ... ok
Bio.SeqUtils.ProtParamData docstring test ... ok
Bio.SeqUtils.lcc docstring test ... ok
Bio.Sequencing docstring test ... ok
Bio.Sequencing.Ace docstring test ... ok
Bio.Sequencing.Applications docstring test ... ok
Bio.Sequencing.Applications._Novoalign docstring test ... ok
Bio.Sequencing.Applications._bwa docstring test ... ok
Bio.Sequencing.Applications._samtools docstring test ... ok
Bio.Sequencing.Phd docstring test ... ok
Bio.SwissProt docstring test ... ok
Bio.SwissProt.KeyWList docstring test ... ok
Bio.UniGene docstring test ... ok
Bio.UniProt.GOA docstring test ... ok
Bio._utils docstring test ... ok
Bio.bgzf docstring test ... ok
Bio.codonalign docstring test ... ok
Bio.codonalign.codonalignment docstring test ... ok
Bio.codonalign.codonseq docstring test ... ok
Bio.cpairwise2 docstring test ... ok
Bio.kNN docstring test ... ok
Bio.motifs docstring test ... ok
Bio.motifs._pwm docstring test ... ok
Bio.motifs.alignace docstring test ... ok
Bio.motifs.applications docstring test ... ok
Bio.motifs.applications._xxmotif docstring test ... ok
Bio.motifs.clusterbuster docstring test ... ok
Bio.motifs.jaspar docstring test ... ok
Bio.motifs.jaspar.db docstring test ... ok
Bio.motifs.mast docstring test ... ok
Bio.motifs.matrix docstring test ... ok
Bio.motifs.meme docstring test ... ok
Bio.motifs.minimal docstring test ... ok
Bio.motifs.pfm docstring test ... ok
Bio.motifs.thresholds docstring test ... ok
Bio.motifs.transfac docstring test ... ok
Bio.motifs.xms docstring test ... ok
Bio.pairwise2 docstring test ... ok
Bio.phenotype docstring test ... ok
Bio.phenotype.phen_micro docstring test ... ok
Bio.phenotype.pm_fitting docstring test ... ok
BioSQL docstring test ... ok
BioSQL.BioSeq docstring test ... ok
BioSQL.BioSeqDatabase docstring test ... ok
BioSQL.DBUtils docstring test ... ok
BioSQL.Loader docstring test ... ok
======================================================================
FAIL: test_mem (test_BWA_tool.BwaTestCase.test_mem)
Test for generating samfile by paired end sequencing using BWA-MEM.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Tests/test_BWA_tool.py",
line 203, in test_mem
self.assertTrue(
~~~~~~~~~~~~~~~^
headline.startswith("@SQ"),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
AssertionError: False is not true : Error generating sam files:
bwa mem BWA/human_g1k_v37_truncated.fasta BWA/HNSCC1_1_truncated.fastq
BWA/HNSCC1_2_truncated.fastq
Output starts:@HD VN:1.5 SO:unsorted GO:query
======================================================================
FAIL: test_sampe (test_BWA_tool.BwaTestCase.test_sampe)
Test for generating samfile by paired end sequencing.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Tests/test_BWA_tool.py",
line 186, in test_sampe
self.assertTrue(
~~~~~~~~~~~~~~~^
headline.startswith("@SQ"),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
AssertionError: False is not true : Error generating sam files:
bwa sampe BWA/human_g1k_v37_truncated.fasta BWA/1.sai BWA/2.sai
BWA/HNSCC1_1_truncated.fastq BWA/HNSCC1_2_truncated.fastq
Output starts:@HD VN:1.5 SO:unsorted GO:query
======================================================================
FAIL: test_samse (test_BWA_tool.BwaTestCase.test_samse)
Test for single end sequencing.
----------------------------------------------------------------------
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Tests/test_BWA_tool.py",
line 163, in test_samse
self.assertTrue(
~~~~~~~~~~~~~~~^
headline.startswith("@SQ"),
^^^^^^^^^^^^^^^^^^^^^^^^^^^
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
AssertionError: False is not true : Error generating sam files:
bwa samse BWA/human_g1k_v37_truncated.fasta BWA/1.sai
BWA/HNSCC1_1_truncated.fastq
Output starts:@HD VN:1.5 SO:unsorted GO:query
----------------------------------------------------------------------
Ran 552 tests in 326.188 seconds
FAILED (failures = 1)
Skipping any tests requiring internet access
Python version: 3.13.7 (main, Aug 20 2025, 22:17:40) [GCC 14.3.0]
Operating system: posix linux
E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: \
set -e; \
mkdir -p /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/home; \
mkdir -p
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Doc/examples; \
cp -a Doc/Tutorial
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Doc; \
cp -a Doc/examples
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Doc; \
cp -a Tests /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; \
cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Tests; \
env DIALIGN2_DIR=/usr/share/dialign \
EMBOSS_ROOT=/usr/lib/emboss \
HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/home \
python3.13 run_tests.py --offline
rm -fr -- /tmp/dh-xdg-rundir-cSYt3yOG
dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test
--system=custom "--test-args= \\\
set -e; \\\
mkdir -p {build_dir}/home; \\\
mkdir -p {build_dir}/Doc/examples; \\\
cp -a Doc/Tutorial {build_dir}/Doc; \\\
cp -a Doc/examples {build_dir}/Doc; \\\
cp -a Tests {build_dir}; \\\
cd {build_dir}/Tests; \\\
env DIALIGN2_DIR=/usr/share/dialign \\\
EMBOSS_ROOT=/usr/lib/emboss \\\
HOME={build_dir}/home \\\
{interpreter} run_tests.py --offline" returned exit
code 13
make[1]: *** [debian/rules:124: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:72: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.85+dfsg-5
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-biopython, 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-biopython
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, 13 Sep 2025 12:12:17 +0200
Source: python-biopython
Architecture: source
Version: 1.85+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1103472 1114298
Changes:
python-biopython (1.85+dfsg-5) unstable; urgency=medium
.
* bwa-output.patch: new: fix a test failure. (Closes: #1114298)
* d/control: build depends on python3-numpy-dev:any.
Lintian flagged that dh_numpy3 needed python3-numpy-dev:any.
* d/watch: update to file format version 5.
* d/patches/*: normalize dep3 headers.
* d/python3-biopython.lintian-overrides: delete.
The spelling override that was within is not needed anymore.
* d/control: uncondionally deploy some build-dependencies.
Several of the packages that were initially marked as <!nocheck>
turned out to be actually needed outside check context. (Closes: #1103472)
* d/rules: isolate a code segment irrelevant with nocheck profile.
Checksums-Sha1:
b75a3c3be9de7b40aac86747c99d0e0ad581a322 3562 python-biopython_1.85+dfsg-5.dsc
282d87343b8e1ef766a4bbaec441323b34128981 43332
python-biopython_1.85+dfsg-5.debian.tar.xz
Checksums-Sha256:
ce852a2baf75a561cd81ddc7a1277c9dff7503ab6c25e80bf44bccbbbe0b9478 3562
python-biopython_1.85+dfsg-5.dsc
19a95127c98d26a34cf84c7ea168c24f250ecad6f41d6399dafebd98b0699b40 43332
python-biopython_1.85+dfsg-5.debian.tar.xz
Files:
504cc588e5ae8837e4c9a45295ba3408 3562 python optional
python-biopython_1.85+dfsg-5.dsc
bf139def4339acdc243382f89405f6cd 43332 python optional
python-biopython_1.85+dfsg-5.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=bAXk
-----END PGP SIGNATURE-----
pgpV60mnpfWId.pgp
Description: PGP signature
--- End Message ---
