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Groups > linux.debian.bugs.rc > #396904 > unrolled thread
| Started by | Santiago Vila <sanvila@debian.org> |
|---|---|
| First post | 2025-09-05 20:40 +0200 |
| Last post | 2025-09-14 02:10 +0200 |
| Articles | 6 — 4 participants |
Back to article view | Back to linux.debian.bugs.rc
Bug#1114298: python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\ Santiago Vila <sanvila@debian.org> - 2025-09-05 20:40 +0200
Bug#1114298: python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\ Étienne Mollier <emollier@debian.org> - 2025-09-13 10:20 +0200
Processed: Re: Bug#1114298: python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\ "Debian Bug Tracking System" <owner@bugs.debian.org> - 2025-09-13 10:20 +0200
Processed: Bug#1114298 marked as pending in python-biopython "Debian Bug Tracking System" <owner@bugs.debian.org> - 2025-09-13 12:50 +0200
Bug#1114298: marked as pending in python-biopython Étienne Mollier <noreply@salsa.debian.org> - 2025-09-13 12:50 +0200
Bug#1114298: marked as done (python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\) "Debian Bug Tracking System" <owner@bugs.debian.org> - 2025-09-14 02:10 +0200
| From | Santiago Vila <sanvila@debian.org> |
|---|---|
| Date | 2025-09-05 20:40 +0200 |
| Subject | Bug#1114298: python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\ |
| Message-ID | <LrJvQ-d415-5@gated-at.bofh.it> |
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
--------------------------------------------------------------------------------
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| From | Étienne Mollier <emollier@debian.org> |
|---|---|
| Date | 2025-09-13 10:20 +0200 |
| Message-ID | <LutEd-eXPU-1@gated-at.bofh.it> |
| In reply to | #396904 |
[Multipart message — attachments visible in raw view] — view raw
Control: tags -1 + upstream patch
Hi Santiago,
Thanks for your report! Concerning the main issue of the entry,
it looks to be caused by a change in bwa 0.7.19, uploaded in sid
last month. I managed to get somewhere with this workaround:
-------8<--------------8<--------------8<--------------8<-------
--- python-biopython.orig/Tests/test_BWA_tool.py
+++ python-biopython/Tests/test_BWA_tool.py
@@ -161,7 +161,7 @@
with open(self.samfile1) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ") or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
)
@@ -184,7 +184,7 @@
with open(self.samfile) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ") or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
)
@@ -201,7 +201,7 @@
with open(self.samfile) as handle:
headline = handle.readline()
self.assertTrue(
- headline.startswith("@SQ"),
+ headline.startswith("@SQ" or headline.startswith("@HD"),
f"Error generating sam files:\n{cmdline}\nOutput starts:{headline}",
)
-------8<--------------8<--------------8<--------------8<-------
Regarding your secondary remark:
> Note: In addition to this package failing to build in unstable six
> days ago, it also fails to build in bookworm right now.
the relevant part of the symptoms is different:
self.perform_test(
File "/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 631, in perform_test
self.check_simple_write_read(
File "/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Tests/test_SeqIO.py", line 367, in check_simple_write_read
records2 = list(SeqIO.parse(handle=handle, format=fmt))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/Interfaces.py", line 72, in __next__
return next(self.records)
^^^^^^^^^^^^^^^^^^
File "/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 448, in iterate
parser.close()
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 240, in close
self.feed(b"", isFinal=True)
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 217, in feed
self._parser.Parse(data, isFinal)
File "../Modules/pyexpat.c", line 416, in StartElement
File "/usr/lib/python3.11/xml/sax/expatreader.py", line 369, in start_element_ns
self._cont_handler.startElementNS(pair, None,
File "/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 164, in startEntryFieldElement
return self.startPropertyElement(attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/build/reproducible-path/python-biopython-1.80+dfsg/.pybuild/cpython3_3.11/build/Bio/SeqIO/SeqXmlIO.py", line 340, in startPropertyElement
record = self.records[-1]
~~~~~~~~~~~~^^^^
IndexError: list index out of range
The issue does ring a bell though and I believe it stems from
Debian 12.12's libxml2 upgrade to address a few CVEs, as
documented in the official announcement[1].
[1]: https://lists.debian.org/debian-stable-announce/2025/09/msg00001.html
Have a nice day, :)
--
.''`. Étienne Mollier <emollier@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/3, please excuse my verbosity
`-
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| From | "Debian Bug Tracking System" <owner@bugs.debian.org> |
|---|---|
| Date | 2025-09-13 10:20 +0200 |
| Subject | Processed: Re: Bug#1114298: python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\ |
| Message-ID | <LutEd-eXPU-9@gated-at.bofh.it> |
| In reply to | #396904 |
Processing control commands:
> tags -1 + upstream patch
Bug #1114298 [src:python-biopython] python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\
Added tag(s) patch and upstream.
--
1114298: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114298
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
[toc] | [prev] | [next] | [standalone]
| From | "Debian Bug Tracking System" <owner@bugs.debian.org> |
|---|---|
| Date | 2025-09-13 12:50 +0200 |
| Subject | Processed: Bug#1114298 marked as pending in python-biopython |
| Message-ID | <LuvZn-eZds-3@gated-at.bofh.it> |
| In reply to | #396904 |
Processing control commands:
> tag -1 pending
Bug #1114298 [src:python-biopython] python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\
Added tag(s) pending.
--
1114298: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114298
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
[toc] | [prev] | [next] | [standalone]
| From | Étienne Mollier <noreply@salsa.debian.org> |
|---|---|
| Date | 2025-09-13 12:50 +0200 |
| Subject | Bug#1114298: marked as pending in python-biopython |
| Message-ID | <LuvZn-eZds-5@gated-at.bofh.it> |
| In reply to | #396904 |
Control: tag -1 pending Hello, Bug #1114298 in python-biopython reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/med-team/python-biopython/-/commit/44adacb57e7f113bba87e1fb1585559da65ac62a ------------------------------------------------------------------------ bwa-output.patch: new: fix a test failure. Closes: #1114298 ------------------------------------------------------------------------ (this message was generated automatically) -- Greetings https://bugs.debian.org/1114298
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| From | "Debian Bug Tracking System" <owner@bugs.debian.org> |
|---|---|
| Date | 2025-09-14 02:10 +0200 |
| Subject | Bug#1114298: marked as done (python-biopython: FTBFS: dh_auto_test: error: pybuild --test -i python{version} -p 3.13 --test --system=custom "--test-args= \\) |
| Message-ID | <LuItz-f7D0-3@gated-at.bofh.it> |
| In reply to | #396904 |
[Multipart message — attachments visible in raw view] — view raw
Your message dated Sun, 14 Sep 2025 00:08:15 +0000
with message-id <E1uxaHv-004QDX-39@fasolo.debian.org>
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 owner@bugs.debian.org
immediately.)
--
1114298: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114298
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
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