Your message dated Sun, 14 Sep 2025 00:08:15 +0000
with message-id <[email protected]>
and subject line Bug#1103472: fixed in python-biopython 1.85+dfsg-5
has caused the Debian Bug report #1103472,
regarding python-biopython: 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.)
--
1103472: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103472
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:python-biopython
Version: 1.85+dfsg-4
Severity: important
Tags: trixie 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:
--------------------------------------------------------------------------------
[...]
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.
!!
********************************************************************************
[... snipped ...]
reading sources... [ 82%] api/Bio.SeqIO.QualityIO
reading sources... [ 82%] api/Bio.SeqIO.SeqXmlIO
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reading sources... [ 91%] api/Bio.codonalign
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Bio/codonalign/__init__.py:21:
BiopythonExperimentalWarning: Bio.codonalign is an experimental module which
may undergo significant changes prior to its future official release.
warnings.warn(
reading sources... [ 91%] api/Bio.codonalign.codonalignment
reading sources... [ 92%] api/Bio.codonalign.codonseq
reading sources... [ 92%] api/Bio.kNN
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Bio/kNN.py:46:
BiopythonDeprecationWarning: The 'Bio.kNN' module is deprecated and will be
removed in a future release of Biopython. Consider using scikit-learn instead.
warnings.warn(
reading sources... [ 92%] api/Bio.motifs
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reading sources... [ 97%] api/Bio.pairwise2
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/Bio/pairwise2.py:278:
BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend
to remove it in a future release of Biopython. As an alternative, please
consider using Bio.Align.PairwiseAligner as a replacement, and contact the
Biopython developers if you still need the Bio.pairwise2 module.
warnings.warn(
reading sources... [ 97%] api/Bio.phenotype
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reading sources... [ 99%] api/BioSQL.DBUtils
reading sources... [ 99%] api/BioSQL.Loader
reading sources... [100%] api/index
reading sources... [100%] index
WARNING: autodoc: failed to import module 'Graphics' from module 'Bio'; the
following exception was raised:
Please install ReportLab if you want to use Bio.Graphics. You can find
ReportLab at http://www.reportlab.com/software/opensource/
[autodoc.import_object]
WARNING: autodoc: failed to import module 'Graphics.BasicChromosome' from
module 'Bio'; the following exception was raised:
Please install ReportLab if you want to use Bio.Graphics. You can find
ReportLab at http://www.reportlab.com/software/opensource/
[autodoc.import_object]
WARNING: autodoc: failed to import module 'Graphics.ColorSpiral' from module
'Bio'; the following exception was raised:
Please install ReportLab if you want to use Bio.Graphics. You can find
ReportLab at http://www.reportlab.com/software/opensource/
[autodoc.import_object]
WARNING: autodoc: failed to import module 'Graphics.Comparative' from module
'Bio'; the following exception was raised:
Please install ReportLab if you want to use Bio.Graphics. You can find
ReportLab at http://www.reportlab.com/software/opensource/
[autodoc.import_object]
WARNING: autodoc: failed to import module 'Graphics.DisplayRepresentation' from
module 'Bio'; the following exception was raised:
Please install ReportLab if you want to use Bio.Graphics. You can find
ReportLab at http://www.reportlab.com/software/opensource/
[autodoc.import_object]
WARNING: autodoc: failed to import module 'Graphics.Distribution' from module
'Bio'; the following exception was raised:
Please install ReportLab if you want to use Bio.Graphics. You can find
ReportLab at http://www.reportlab.com/software/opensource/
[autodoc.import_object]
WARNING: autodoc: failed to import module 'Graphics.GenomeDiagram' from module
'Bio'; the following exception was raised:
Please install ReportLab if you want to use Bio.Graphics. You can find
ReportLab at http://www.reportlab.com/software/opensource/
[autodoc.import_object]
WARNING: autodoc: failed to import module 'Graphics.KGML_vis' from module
'Bio'; the following exception was raised:
Please install ReportLab if you want to use Bio.Graphics. You can find
ReportLab at http://www.reportlab.com/software/opensource/
[autodoc.import_object]
WARNING: autodoc: failed to import module 'binary_cif' from module 'Bio.PDB';
the following exception was raised:
Install msgpack to use Bio.PDB.binaryCIF (e.g. pip install msgpack)
[autodoc.import_object]
WARNING: autodoc: failed to import module 'mmtf' from module 'Bio.PDB'; the
following exception was raised:
Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
[autodoc.import_object]
WARNING: autodoc: failed to import module 'mmtf.DefaultParser' from module
'Bio.PDB'; the following exception was raised:
Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
[autodoc.import_object]
WARNING: autodoc: failed to import module 'mmtf.mmtfio' from module 'Bio.PDB';
the following exception was raised:
Install mmtf to use Bio.PDB.mmtf (e.g. pip install mmtf-python)
[autodoc.import_object]
WARNING: autodoc: failed to import module 'CDAOIO' from module 'Bio.Phylo'; the
following exception was raised:
Support for CDAO tree format requires RDFlib. [autodoc.import_object]
WARNING: autodoc: failed to import module 'pm_fitting' from module
'Bio.phenotype'; the following exception was raised:
Install scipy to extract curve parameters. [autodoc.import_object]
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
copying assets...
copying static files...
Writing evaluated template result to
/<<PKGBUILDDIR>>/Doc/_build/html/_static/language_data.js
Writing evaluated template result to
/<<PKGBUILDDIR>>/Doc/_build/html/_static/documentation_options.js
Writing evaluated template result to
/<<PKGBUILDDIR>>/Doc/_build/html/_static/basic.css
Writing evaluated template result to
/<<PKGBUILDDIR>>/Doc/_build/html/_static/js/versions.js
copying static files: done
copying extra files...
copying extra files: done
copying assets: done
writing output... [ 0%] Tutorial/chapter_align
writing output... [ 1%] Tutorial/chapter_appendix
writing output... [ 1%] Tutorial/chapter_bibliography
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writing output... [ 2%] Tutorial/chapter_contributing
writing output... [ 2%] Tutorial/chapter_cookbook
writing output... [ 3%] Tutorial/chapter_entrez
writing output... [ 3%] Tutorial/chapter_graphics
writing output... [ 3%] Tutorial/chapter_introduction
writing output... [ 4%] Tutorial/chapter_kegg
writing output... [ 4%] Tutorial/chapter_motifs
writing output... [ 4%] Tutorial/chapter_msa
writing output... [ 5%] Tutorial/chapter_pairwise
writing output... [ 5%] Tutorial/chapter_pairwise2
writing output... [ 5%] Tutorial/chapter_pdb
writing output... [ 6%] Tutorial/chapter_phenotype
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writing output... [ 7%] Tutorial/chapter_searchio
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writing output... [ 8%] Tutorial/chapter_testing
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writing output... [ 57%] api/Bio.PDB.parse_pdb_header
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writing output... [ 59%] api/Bio.Phylo
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writing output... [ 92%] api/Bio.motifs
writing output... [ 93%] api/Bio.motifs.alignace
writing output... [ 93%] api/Bio.motifs.applications
writing output... [ 93%] api/Bio.motifs.clusterbuster
writing output... [ 94%] api/Bio.motifs.jaspar
writing output... [ 94%] api/Bio.motifs.jaspar.db
writing output... [ 94%] api/Bio.motifs.mast
writing output... [ 94%] api/Bio.motifs.matrix
writing output... [ 95%] api/Bio.motifs.meme
writing output... [ 95%] api/Bio.motifs.minimal
writing output... [ 95%] api/Bio.motifs.pfm
writing output... [ 96%] api/Bio.motifs.thresholds
writing output... [ 96%] api/Bio.motifs.transfac
writing output... [ 96%] api/Bio.motifs.xms
writing output... [ 97%] api/Bio.pairwise2
writing output... [ 97%] api/Bio.phenotype
writing output... [ 97%] api/Bio.phenotype.phen_micro
writing output... [ 98%] api/Bio.phenotype.pm_fitting
writing output... [ 98%] api/BioSQL
writing output... [ 98%] api/BioSQL.BioSeq
writing output... [ 99%] api/BioSQL.BioSeqDatabase
writing output... [ 99%] api/BioSQL.DBUtils
writing output... [ 99%] api/BioSQL.Loader
writing output... [100%] api/index
writing output... [100%] index
generating indices... genindex py-modindex done
writing additional pages... search done
copying images... [ 4%] images/BlastRecord.png
copying images... [ 7%] images/PSIBlastRecord.png
copying images... [ 11%] images/hist_plot.png
copying images... [ 14%] images/gc_plot.png
copying images... [ 18%] images/dot_plot.png
copying images... [ 21%] images/dot_plot_scatter.png
copying images... [ 25%] images/SRR001666.png
copying images... [ 29%] images/plasmid_linear.png
copying images... [ 32%] images/plasmid_circular.png
copying images... [ 36%] images/GD_sigil_labels.png
copying images... [ 39%] images/GD_sigils.png
copying images... [ 43%] images/GD_sigil_arrow_shafts.png
copying images... [ 46%] images/GD_sigil_arrow_heads.png
copying images... [ 50%] images/plasmid_linear_nice.png
copying images... [ 54%] images/plasmid_circular_nice.png
copying images... [ 57%] images/three_track_simple.png
copying images... [ 61%] images/three_track_cl.png
copying images... [ 64%] images/three_track_cl2a.png
copying images... [ 68%] images/simple_chrom.png
copying images... [ 71%] images/tRNA_chrom.png
copying images... [ 75%] images/biopython_logo_m.png
copying images... [ 79%] images/biopython_logo_old.jpg
copying images... [ 82%] images/smcra.png
copying images... [ 86%] images/1a8o-ca-plot.png
copying images... [ 89%] images/phe-pairs-3pbl.png
copying images... [ 93%] images/phylo-simple-draw.png
copying images... [ 96%] images/phylo-color-draw.png
copying images... [100%] images/phylo-draw-example.png
dumping search index in English (code: en)... done
dumping object inventory... done
build finished with problems, 14 warnings (with warnings treated as errors).
make[2]: *** [Makefile:20: html] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/Doc'
make[1]: *** [debian/rules:95: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:72: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202504/
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.
Notes:
* When a package is built with the nocheck profile, it means:
- DEB_BUILD_OPTIONS=nocheck
(the tests should be skipped during the build)
- DEB_BUILD_PROFILES=nocheck
(Build-Depends marked <!nocheck> are not installed)
* This category of bugs was going to be RC for trixie, but
according to the Release Managers it's a little bit late in the
release cycle to introduce a bunch of RC bugs of this type.
* In addition to the above, this package also fails when
using DEB_BUILD_OPTIONS=nocheck alone. In this mode:
- DEB_BUILD_OPTIONS=nocheck
(the tests should be skipped during the build)
- Build-Depends marked <!nocheck> are installed as normal
Note that in both modes of building the contents of the package
is not expected to change compared to a regular build.
Thanks.
--- 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.
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