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