[Debian-med-packaging] Bug#1103472: python-biopython: FTBFS with the nocheck build profile

Santiago Vila sanvila at debian.org
Fri Apr 18 00:17:16 BST 2025 

Package: src:python-biopython
Version: 1.85+dfsg-4
Severity: important
Tags: trixie sid ftbfs
User: debian-qa at lists.debian.org
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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/<<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(
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/<<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(
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/<<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(
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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
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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.

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