Package: src:pybel Version: 0.15.5-4 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202609/ 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 cannot 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:pybel, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ tests/test_cli.py:13: in <module> from pybel import Manager, cli pybel/cli.py:24: in <module> from pkg_resources import iter_entry_points E ModuleNotFoundError: No module named 'pkg_resources' =============================== warnings summary =============================== pybel/manager/models.py:91 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/manager/models.py:91: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9) Base = declarative_base() pybel/parser/utils.py:53 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/utils.py:53: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' quote = dblQuotedString().setParseAction(removeQuotes) pybel/parser/utils.py:55 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/utils.py:55: PyparsingDeprecationWarning: 'delimitedList' deprecated - use 'DelimitedList' delimited_quoted_list = And([Suppress("{"), delimitedList(quote), Suppress("}")]) pybel/parser/utils.py:56 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/utils.py:56: PyparsingDeprecationWarning: 'delimitedList' deprecated - use 'DelimitedList' delimited_unquoted_list = And([Suppress("{"), delimitedList(identifier), Suppress("}")]) pybel/parser/utils.py:82: 34 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/utils.py:82: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' element = oneOf(tags).setParseAction(replaceWith(canonical_tag)) pybel/parser/utils.py:82: 34 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/utils.py:82: PyparsingDeprecationWarning: 'replaceWith' deprecated - use 'replace_with' element = oneOf(tags).setParseAction(replaceWith(canonical_tag)) pybel/parser/utils.py:82: 34 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/utils.py:82: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' element = oneOf(tags).setParseAction(replaceWith(canonical_tag)) pybel/parser/utils.py:87: 23 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/utils.py:87: PyparsingDeprecationWarning: 'setResultsName' deprecated - use 'set_results_name' return element.setResultsName(name) pybel/parser/modifiers/fusion.py:65 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/fusion.py:65: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' fusion_tags = oneOf(["fus", "fusion"]).setParseAction(replaceWith(FUSION)) pybel/parser/modifiers/fusion.py:65 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/fusion.py:65: PyparsingDeprecationWarning: 'replaceWith' deprecated - use 'replace_with' fusion_tags = oneOf(["fus", "fusion"]).setParseAction(replaceWith(FUSION)) pybel/parser/modifiers/fusion.py:65 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/fusion.py:65: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' fusion_tags = oneOf(["fus", "fusion"]).setParseAction(replaceWith(FUSION)) pybel/parser/modifiers/fusion.py:66 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/fusion.py:66: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' reference_seq = oneOf(["r", "p", "c"]) pybel/parser/modifiers/gene_modification.py:65 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/gene_modification.py:65: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' gmod_default_ns = oneOf(list(gmod_namespace)).setParseAction(_handle_gmod_default) pybel/parser/modifiers/gene_modification.py:65 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/gene_modification.py:65: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' gmod_default_ns = oneOf(list(gmod_namespace)).setParseAction(_handle_gmod_default) pybel/parser/modifiers/gene_substitution.py:48 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/gene_substitution.py:48: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' dna_nucleotide = oneOf(list(language.dna_nucleotide_labels.keys())) pybel/parser/modifiers/location.py:56 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/location.py:56: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' location_tag = Suppress(oneOf(["loc", "location"])) pybel/parser/modifiers/constants.py:10 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/constants.py:10: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' aa_single = oneOf(list(language.amino_acid_dict.keys())) pybel/parser/modifiers/constants.py:11 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/constants.py:11: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' aa_single.setParseAction(lambda s, l, t: [language.amino_acid_dict[t[0]]]) pybel/parser/modifiers/constants.py:13 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/constants.py:13: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' aa_triple = oneOf(list(language.amino_acid_dict.values())) pybel/parser/modifiers/constants.py:25 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/constants.py:25: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' aa_placeholder.setParseAction(handle_aa_placeholder) pybel/parser/modifiers/protein_modification.py:123 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/protein_modification.py:123: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' pmod_default_ns = oneOf(list(pmod_namespace)).setParseAction(_handle_pmod_default_ns) pybel/parser/modifiers/protein_modification.py:123 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/protein_modification.py:123: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' pmod_default_ns = oneOf(list(pmod_namespace)).setParseAction(_handle_pmod_default_ns) pybel/parser/modifiers/protein_modification.py:124 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/protein_modification.py:124: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' pmod_legacy_ns = oneOf(list(pmod_legacy_labels)).setParseAction(_handle_pmod_legacy_ns) pybel/parser/modifiers/protein_modification.py:124 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/protein_modification.py:124: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' pmod_legacy_ns = oneOf(list(pmod_legacy_labels)).setParseAction(_handle_pmod_legacy_ns) pybel/parser/parse_control.py:55 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_control.py:55: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' supporting_text_tags = oneOf([BEL_KEYWORD_EVIDENCE, BEL_KEYWORD_SUPPORT]) pybel/parser/modifiers/protein_substitution.py:59 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/protein_substitution.py:59: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' parser_element.setParseAction(_handle_psub) pybel/parser/modifiers/gene_substitution.py:59 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/gene_substitution.py:59: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' parser_element.setParseAction(_handle_gsub) pybel/parser/modifiers/truncation.py:61 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/truncation.py:61: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' l1.setParseAction(_handle_trunc) pybel/parser/modifiers/truncation.py:63 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/modifiers/truncation.py:63: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' l2.setParseAction(_handle_trunc_legacy) pybel/parser/parse_bel.py:191 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:191: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' molecular_activity_tags = Suppress(oneOf(["ma", "molecularActivity"])) pybel/parser/parse_bel.py:217 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:217: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' increases_tag = oneOf(["->", "â", "increases"]).setParseAction(replaceWith(INCREASES)) pybel/parser/parse_bel.py:217 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:217: PyparsingDeprecationWarning: 'replaceWith' deprecated - use 'replace_with' increases_tag = oneOf(["->", "â", "increases"]).setParseAction(replaceWith(INCREASES)) pybel/parser/parse_bel.py:217 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:217: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' increases_tag = oneOf(["->", "â", "increases"]).setParseAction(replaceWith(INCREASES)) pybel/parser/parse_bel.py:259 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:259: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' transcribed_tag = oneOf([":>", "transcribedTo"]).setParseAction(replaceWith(TRANSCRIBED_TO)) pybel/parser/parse_bel.py:259 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:259: PyparsingDeprecationWarning: 'replaceWith' deprecated - use 'replace_with' transcribed_tag = oneOf([":>", "transcribedTo"]).setParseAction(replaceWith(TRANSCRIBED_TO)) pybel/parser/parse_bel.py:259 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:259: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' transcribed_tag = oneOf([":>", "transcribedTo"]).setParseAction(replaceWith(TRANSCRIBED_TO)) pybel/parser/parse_bel.py:262 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:262: PyparsingDeprecationWarning: 'oneOf' deprecated - use 'one_of' translated_tag = oneOf([">>", "translatedTo"]).setParseAction(replaceWith(TRANSLATED_TO)) pybel/parser/parse_bel.py:262 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:262: PyparsingDeprecationWarning: 'replaceWith' deprecated - use 'replace_with' translated_tag = oneOf([">>", "translatedTo"]).setParseAction(replaceWith(TRANSLATED_TO)) pybel/parser/parse_bel.py:262 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/parser/parse_bel.py:262: PyparsingDeprecationWarning: 'setParseAction' deprecated - use 'set_parse_action' translated_tag = oneOf([">>", "translatedTo"]).setParseAction(replaceWith(TRANSLATED_TO)) pybel/schema/__init__.py:29 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/schema/__init__.py:29: DeprecationWarning: pathlib.PurePath.as_uri() is deprecated and scheduled for removal in Python 3.19. Use pathlib.Path.as_uri(). schema_uri = pathlib.PurePath(__file__).as_uri() pybel/schema/__init__.py:30 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build/pybel/schema/__init__.py:30: DeprecationWarning: jsonschema.RefResolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. A future release will remove RefResolver. Please file a feature request (on referencing) if you are missing an API for the kind of customization you need. RESOLVER = jsonschema.RefResolver(base_uri=schema_uri, referrer=__file__) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ ERROR tests/test_bel_repository.py ERROR tests/test_cli.py !!!!!!!!!!!!!!!!!!! Interrupted: 2 errors during collection !!!!!!!!!!!!!!!!!!!! =============== 171 deselected, 162 warnings, 2 errors in 1.16s ================ E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pybel/build; python3.14 -m pytest --ignore=tests/test_grounding.py -k ' not test_seeding and not test_import and not test_manager_graph and not test_insert_namespace_persistent and not test_parse_metadata and not test_bel_simple and not test_bel_thorough and not test_update_matrix_activation and not test_update_matrix_activation_phosphorylation and not test_update_matrix_activation_ubiquination and not test_update_matrix_association and not test_update_matrix_expression and not test_update_matrix_inhibition and not test_update_matrix_inhibition_phosphorylation and not test_update_matrix_inhibition_ubiquination and not test_update_matrix_pmods and not test_update_matrix_repression and not test_reset_citation and not test_set_regex and not test_get_random_path ' dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.14 --parallel=2 returned exit code 13 make: *** [debian/rules:31: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
