[Debian-med-packaging] Bug#1116836: pdb2pqr: FTBFS with the nocheck build profile

Santiago Vila sanvila at debian.org
Tue Sep 30 15:52:35 BST 2025 

Package: src:pdb2pqr
Version: 3.6.1+dfsg-1
Severity: important
Tags: forky 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.

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/

A wiki page discussing how to reproduce bugs in this category and
possible solutions is available here:

https://wiki.debian.org/qa.debian.org/FTBFS/Nocheck

(It's a wiki, so you are welcome to contribute)

[ Note: This is RC, but I will wait at least two weeks before raising
the severities, there are a lot of gcc-15 and CMake 4 bugs open now ].

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:pdb2pqr, so that this is still
visible in the BTS web page for this package.

Thanks.

--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem pybuild --with python3
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
I: pybuild base:311: python3.13 setup.py clean 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/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 :: OSI Approved :: BSD License

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  self._finalize_license_expression()
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.13' does not exist -- can't clean it
rm -rf pdb2pqr.egg-info
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --buildsystem pybuild --with python3
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:311: python3.13 setup.py config 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/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 :: OSI Approved :: BSD License

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  self._finalize_license_expression()
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:311: /usr/bin/python3 setup.py build 
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'tests_require'
  warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite'
  warnings.warn(msg)
/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 :: OSI Approved :: BSD License

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!
  self._finalize_license_expression()
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/structures.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/definitions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/forcefield.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/cells.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/psize.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/config.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/run.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/pdb.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/inputgen.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/io.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/aa.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/biomolecule.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/main.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/na.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/residue.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/utilities.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/debump.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/cif.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/topology.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
copying pdb2pqr/quatfit.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
copying pdb2pqr/ligand/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
copying pdb2pqr/ligand/peoe.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
copying pdb2pqr/ligand/mol2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
copying pdb2pqr/ligand/topology.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/ligand
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/structures.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens
copying pdb2pqr/hydrogens/optimize.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/hydrogens
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/NA.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PATCHES.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/TOPOLOGY.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/HYDROGENS.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/AA.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PARSE.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PEOEPB.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/SWANSON.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/CHARMM.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/TYL06.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/AMBER.DAT -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/TYL06.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/SWANSON.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PARSE.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/CHARMM.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/PEOEPB.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
copying pdb2pqr/dat/AMBER.names -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/pdb2pqr/dat
PYTHONPATH=. python3 -m sphinx -N -bhtml docs/source build/html
Running Sphinx v8.2.3

Configuration error!

Versions
========

* Platform:         linux; (Linux-6.12.48+deb13-cloud-amd64-x86_64-with-glibc2.41)
* Python version:   3.13.7 (CPython)
* Sphinx version:   8.2.3
* Docutils version: 0.21.2
* Jinja2 version:   3.1.6
* Pygments version: 2.18.0

Last Messages
=============

None.

Loaded Extensions
=================

None.

Traceback
=========

      File "/usr/lib/python3/dist-packages/sphinx/config.py", line 616, in eval_config_file
        raise ConfigError(msg % traceback.format_exc()) from exc
    sphinx.errors.ConfigError: There is a programmable error in your configuration file:
    
    Traceback (most recent call last):
      File "/usr/lib/python3/dist-packages/sphinx/config.py", line 601, in eval_config_file
        exec(code, namespace)  # NoQA: S102
        ~~~~^^^^^^^^^^^^^^^^^
      File "/<<PKGBUILDDIR>>/docs/source/conf.py", line 18, in <module>
        import pdb2pqr  # noqa: E402
        ^^^^^^^^^^^^^^
      File "/<<PKGBUILDDIR>>/pdb2pqr/__init__.py", line 10, in <module>
        from .main import main
      File "/<<PKGBUILDDIR>>/pdb2pqr/main.py", line 15, in <module>
        import propka.lib
    ModuleNotFoundError: No module named 'propka'


The full traceback has been saved in:
/tmp/sphinx-err-g7kf19yf.log

To report this error to the developers, please open an issue at <https://github.com/sphinx-doc/sphinx/issues/>. Thanks!
Please also report this if it was a user error, so that a better error message can be provided next time.
make[1]: *** [debian/rules:14: override_dh_auto_build] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------

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