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  • Bug#1103196: plip: FTBFS: help2man: can't get `--help' info from /<

    From Santiago Vila@21:1/5 to All on Tue Apr 15 02:30:01 2025
    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.

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Sergio Durigan Junior@21:1/5 to All on Fri Apr 18 22:50:01 2025
    Control: tag -1 pending

    Hello,

    Bug #1103196 in plip reported by you has been fixed in the
    Git repository and is awaiting an upload. You can see the commit
    message below and you can check the diff of the fix at:

    https://salsa.debian.org/med-team/plip/-/commit/49a6bdfc93617e9b8d656ea4b7d7c22fe5999c38

    ------------------------------------------------------------------------ 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 ------------------------------------------------------------------------

    (this message was generated automatically)
    --
    Greetings

    https://bugs.debian.org/1103196

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Debian Bug Tracking System@21:1/5 to All on Fri Apr 18 22:50:02 2025
    Processing control commands:

    tag -1 pending
    Bug #1103196 [src:plip] plip: FTBFS: help2man: can't get `--help' info from /<<PKGBUILDDIR>>/debian/plip/usr/bin/plipcmd
    Added tag(s) pending.

    --
    1103196: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103196
    Debian Bug Tracking System
    Contact [email protected] with problems

    --- SoupGate-Win32 v1.05
    * Origin: fsxNet Usenet Gateway (21:1/5)
  • From Debian Bug Tracking System@21:1/5 to All on Sat Apr 19 00:00:01 2025
    This is a multi-part message in MIME format...

    Your message dated Fri, 18 Apr 2025 21:48:43 +0000
    with message-id <[email protected]>
    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 [email protected]
    immediately.)


    --
    1103196: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103196
    Debian Bug Tracking System
    Contact [email protected] with problems

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