Your message dated Fri, 18 Apr 2025 21:48:43 +0000 with message-id <e1u5tzj-007awz...@fasolo.debian.org> and subject line Bug#1103196: fixed in plip 2.4.0+dfsg-3 has caused the Debian Bug report #1103196, regarding plip: FTBFS: help2man: can't get `--help' info from /<<PKGBUILDDIR>>/debian/plip/usr/bin/plipcmd 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 ow...@bugs.debian.org immediately.) -- 1103196: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103196 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:plip Version: 2.4.0+dfsg-2 Severity: serious Tags: ftbfs trixie sid Dear maintainer: During a rebuild of all packages in unstable, your package failed to build: -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild 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:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2026-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self._enforce_underscore(opt, section) /usr/lib/python3/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. (Affected: plip). By 2026-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self._enforce_underscore(opt, section) /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 :: GNU General Public License v2 (GPLv2) 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_plip/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 .pybuild/ find . -name \*.pyc -exec rm {} \; dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/plip.substvars debian/files rm -fr -- debian/plip/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild pybuild --configure -i python{version} -p 3.13 I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2026-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self._enforce_underscore(opt, section) /usr/lib/python3/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. (Affected: plip). By 2026-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self._enforce_underscore(opt, section) /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 :: GNU General Public License v2 (GPLv2) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config dh_auto_build -O--buildsystem=pybuild pybuild --build -i python{version} -p 3.13 I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2026-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self._enforce_underscore(opt, section) /usr/lib/python3/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. (Affected: plip). By 2026-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self._enforce_underscore(opt, section) /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 :: GNU General Public License v2 (GPLv2) 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_plip/build/plip copying plip/plipcmd.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip copying plip/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange copying plip/exchange/xml.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange copying plip/exchange/json.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange copying plip/exchange/webservices.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange copying plip/exchange/report.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange copying plip/exchange/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic copying plip/basic/parallel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic copying plip/basic/logger.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic copying plip/basic/remote.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic copying plip/basic/config.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic copying plip/basic/supplemental.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic copying plip/basic/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_hydrogen_bonds.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_literature_validated.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_remote_services.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_structure_processing.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_basic_functions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_pi_stacking.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_water_bridges.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_visualization.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_command_line.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_xml_writer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_xml_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_salt_bridges.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_metal_coordination.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/test_intra.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test copying plip/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization copying plip/visualization/pymol.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization copying plip/visualization/chimera.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization copying plip/visualization/visualize.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization copying plip/visualization/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/structure copying plip/structure/preparation.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/structure copying plip/structure/detection.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/structure copying plip/structure/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/structure running build_scripts creating build/scripts-3.13 copying and adjusting plip/plipcmd.py -> build/scripts-3.13 changing mode of build/scripts-3.13/plipcmd.py from 644 to 755 debian/rules override_dh_auto_test make[1]: Entering directory '/<<PKGBUILDDIR>>' # skip all other tests since they require exluded pdb files export PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/; \ debian/tests/xml-parser make[1]: Leaving directory '/<<PKGBUILDDIR>>' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild rm -f -- debian/plip.substvars rm -fr -- debian/.debhelper/generated/plip/ debian/plip/ debian/tmp/ debian/rules override_dh_auto_install make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_install install -m0755 -d /<<BUILDDIR>>/plip-2.4.0\+dfsg/debian/plip pybuild --install -i python{version} -p 3.13 --dest-dir=/<<BUILDDIR>>/plip-2.4.0\+dfsg/debian/plip I: pybuild base:311: /usr/bin/python3 setup.py install --root /<<PKGBUILDDIR>>/debian/plip /usr/lib/python3/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. By 2026-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self._enforce_underscore(opt, section) /usr/lib/python3/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead. !! ******************************************************************************** Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead. (Affected: plip). By 2026-Mar-03, you need to update your project and remove deprecated calls or your builds will no longer be supported. See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. ******************************************************************************** !! opt = self._enforce_underscore(opt, section) /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 :: GNU General Public License v2 (GPLv2) See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() running build running build_py running build_scripts running install_lib creating /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages creating /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip creating /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange/xml.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange/json.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange/webservices.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange/report.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/exchange/__init__.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/plipcmd.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip creating /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic/parallel.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic/logger.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic/remote.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic/config.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic/supplemental.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/basic/__init__.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic creating /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_hydrogen_bonds.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_literature_validated.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_remote_services.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_structure_processing.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_basic_functions.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_pi_stacking.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_water_bridges.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_visualization.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_command_line.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_xml_writer.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_xml_parser.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_salt_bridges.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_metal_coordination.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/test_intra.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/test/__init__.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test creating /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization/pymol.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization/chimera.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization/visualize.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/visualization/__init__.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/__init__.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip creating /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/structure copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/structure/preparation.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/structure copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/structure/detection.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/structure copying /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_plip/build/plip/structure/__init__.py -> /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/structure byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange/xml.py to xml.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange/json.py to json.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange/webservices.py to webservices.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange/report.py to report.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/exchange/__init__.py to __init__.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/plipcmd.py to plipcmd.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic/parallel.py to parallel.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic/logger.py to logger.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic/remote.py to remote.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic/config.py to config.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic/supplemental.py to supplemental.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/basic/__init__.py to __init__.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_hydrogen_bonds.py to test_hydrogen_bonds.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_literature_validated.py to test_literature_validated.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_remote_services.py to test_remote_services.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_structure_processing.py to test_structure_processing.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_basic_functions.py to test_basic_functions.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_pi_stacking.py to test_pi_stacking.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_water_bridges.py to test_water_bridges.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_visualization.py to test_visualization.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_command_line.py to test_command_line.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_xml_writer.py to test_xml_writer.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_xml_parser.py to test_xml_parser.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_salt_bridges.py to test_salt_bridges.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_metal_coordination.py to test_metal_coordination.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/test_intra.py to test_intra.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/test/__init__.py to __init__.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization/pymol.py to pymol.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization/chimera.py to chimera.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization/visualize.py to visualize.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/visualization/__init__.py to __init__.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/__init__.py to __init__.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/structure/preparation.py to preparation.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/structure/detection.py to detection.cpython-313.pyc byte-compiling /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip/structure/__init__.py to __init__.cpython-313.pyc running install_egg_info running egg_info creating plip.egg-info writing plip.egg-info/PKG-INFO writing dependency_links to plip.egg-info/dependency_links.txt writing entry points to plip.egg-info/entry_points.txt writing requirements to plip.egg-info/requires.txt writing top-level names to plip.egg-info/top_level.txt writing manifest file 'plip.egg-info/SOURCES.txt' reading manifest file 'plip.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'plip.egg-info/SOURCES.txt' Copying plip.egg-info to /<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/plip-2.4.0.egg-info Skipping SOURCES.txt running install_scripts creating /<<PKGBUILDDIR>>/debian/plip/usr/bin copying build/scripts-3.13/plipcmd.py -> /<<PKGBUILDDIR>>/debian/plip/usr/bin changing mode of /<<PKGBUILDDIR>>/debian/plip/usr/bin/plipcmd.py to 755 Installing plip script to /<<PKGBUILDDIR>>/debian/plip/usr/bin rm -rvf /<<PKGBUILDDIR>>/debian/plip/usr/bin/plip removed '/<<PKGBUILDDIR>>/debian/plip/usr/bin/plip' mv /<<PKGBUILDDIR>>/debian/plip/usr/bin/plipcmd.py \ /<<PKGBUILDDIR>>/debian/plip/usr/bin/plipcmd mkdir -p /<<PKGBUILDDIR>>/debian/plip/usr/share/man/man1 export PYTHONPATH=/<<PKGBUILDDIR>>/debian/plip/usr/lib/python3.13/dist-packages/:\ /<<PKGBUILDDIR>>/plip/modules; \ help2man --no-info --no-discard-stderr --version-string="2.4.0+dfsg-2" --name='Protein-Ligand Interaction Profiler (PLIP)' \ /<<PKGBUILDDIR>>/debian/plip/usr/bin/plipcmd > /<<PKGBUILDDIR>>/debian/plip/usr/share/man/man1/plipcmd.1 help2man: can't get `--help' info from /<<PKGBUILDDIR>>/debian/plip/usr/bin/plipcmd make[1]: *** [debian/rules:19: override_dh_auto_install] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:6: 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:plip, so that this is still visible in the BTS web page for this package. Thanks.
--- End Message ---
--- Begin Message ---Source: plip Source-Version: 2.4.0+dfsg-3 Done: Sergio Durigan Junior <sergi...@debian.org> We believe that the bug you reported is fixed in the latest version of plip, 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 1103...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Sergio Durigan Junior <sergi...@debian.org> (supplier of updated plip 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 18 Apr 2025 16:42:39 -0400 Source: plip Architecture: source Version: 2.4.0+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Sergio Durigan Junior <sergi...@debian.org> Closes: 1103196 Changes: plip (2.4.0+dfsg-3) unstable; urgency=medium . * Team upload. * d/rules: Rewrite the shebang to deal with fallout from setuptools. setuptools has recently broken how shebangs are generated for scripts (see Debian bug 1103150), and while the right thing to do here would be to use dh_python3's --shebang option, it doesn't work. So let's rewrite the shebang ourselves. (Closes: #1103196) Checksums-Sha1: 3484696592599eedd146cb72895449a2e68bedf6 2123 plip_2.4.0+dfsg-3.dsc 5455e3662653b6ca17b8c929799e8188aa3815f5 6444 plip_2.4.0+dfsg-3.debian.tar.xz 19e02671a09f9a558c346d9524575dd1e0a64f9d 7548 plip_2.4.0+dfsg-3_amd64.buildinfo Checksums-Sha256: 5e86fa9538d0b61a0b4642671ddfbd20f7e45c2cebe9dbef94cd70a7d564bb6b 2123 plip_2.4.0+dfsg-3.dsc 05ec691717bce40b62a859f1ed705d7e803a5ebe9b8f1c4de63888adb983e9fb 6444 plip_2.4.0+dfsg-3.debian.tar.xz 6d2548d9f0315798891296c4f206587d0abf8b47609ae8a40f12339741423190 7548 plip_2.4.0+dfsg-3_amd64.buildinfo Files: 0b6189ce7d23718c95ac32f2f74f29d4 2123 python optional plip_2.4.0+dfsg-3.dsc 276593965e2d1c5671670c80fef50f25 6444 python optional plip_2.4.0+dfsg-3.debian.tar.xz 29fa2d5d85d0ec5566ff049768a2669e 7548 python optional plip_2.4.0+dfsg-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEI3pUsQKHKL8A7zH00Ot2KGX8XjYFAmgCuXAUHHNlcmdpb2Rq QGRlYmlhbi5vcmcACgkQ0Ot2KGX8XjY5YA/+IBG1D/Y3UrEm7Hv+HvndtGFro5lq PHfMQWNbP5+oI9jYIyKciZPxoscwORe/lVCH3XdBwyiYQ1doB8jAvBvOlmsayrTh buv4GJCl+vdcC1JOBN9Yxc8lU80XED1zmI3l7l5zfXk6u9C4erq3feSB8Pa521PG e8+63rj0AuX+CveqF5ohBIhBkOI82wPnUvDaEClgi20OkZrSQnstFzr8wBnXqzow /AJxi+pYPQxuqRyyHyMi+nq27EZ6RVZa2nZkwpgDF1C7mkCyx1KHvdAaYzkgfxi6 Fo62jS1IFvZ4wIIleZBB6WpC3nWjqLEtBQAC2WQm5jNaXYBR9HfCAhMmW4o/I69e zkU/1JXTR+OZLwFu/Qxfo4FfsdM7sGcURcTlQBvYhiLhr3ykM7bh30+rVGGWtjD4 4UnDQIEzvbkZXgAqjctwoPnANnEzcDvA3VANvKDraTAF+fZIXBEarY76Irjbaugs z7sZf5/w+xUBbSms55XHMb+zmiiL23a6novq7siFPT0sewJSvMj/Mjav+HwJ2LWI UkvWjeMiiDhOx5sPSNJZcTns157hSFBT7jq/ER7Rkk/4FHaLN04Z/RL6MOT3NOSB P7ql/PExMvcMZm67Qg63VYS0T0h85MP7zARIl9fYMdArR/Rv4X6i7YaPIUGwdcHy sSoUPsx35Iym8z8= =IcWs -----END PGP SIGNATURE-----
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