Your message dated Wed, 16 Sep 2026 19:18:56 +0000
with message-id <[email protected]>
and subject line Bug#1147885: fixed in pybel 0.15.5-5
has caused the Debian Bug report #1147885,
regarding pybel: FTBFS: E ModuleNotFoundError: No module named 'pkg_resources'
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.)
--
1147885: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1147885
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: pybel
Source-Version: 0.15.5-5
Done: Alexandre Detiste <[email protected]>
We believe that the bug you reported is fixed in the latest version of
pybel, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Alexandre Detiste <[email protected]> (supplier of updated pybel 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 16 Sep 2026 20:51:44 +0200
Source: pybel
Architecture: source
Version: 0.15.5-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Alexandre Detiste <[email protected]>
Closes: 1147885
Changes:
pybel (0.15.5-5) unstable; urgency=medium
.
* Team upload.
* Extend remove-pkg-resources.diff (Closes: #1147885)
* Reformat the Last-Update date as ISO YYYY-MM-DD.
* Update standards version to 4.7.4, no changes needed.
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