Source: python-loompy
Version: 3.0.7+dfsg-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20231212 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> debian/rules binary
> dh binary --with python3 --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 "3.12 3.11"
> I: pybuild base:310: python3.12 setup.py config
> running config
> I: pybuild base:310: python3.11 setup.py config
> running config
> dh_auto_build -O--buildsystem=pybuild
> pybuild --build -i python{version} -p "3.12 3.11"
> I: pybuild base:310: /usr/bin/python3.12 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/utils.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/loom_view.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/cell_calling.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/normalize.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/_version.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/to_html.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/layer_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/loompy.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/graph_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/bus_file.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/loom_validator.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/attribute_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/metadata_loaders.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/loom_layer.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/commands.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/global_attribute_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/view_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> I: pybuild base:310: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/utils.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/__init__.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/loom_view.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/cell_calling.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/normalize.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/_version.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/to_html.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/layer_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/loompy.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/graph_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/bus_file.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/loom_validator.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/attribute_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/metadata_loaders.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/loom_layer.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/commands.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/global_attribute_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/view_manager.py ->
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> dh_auto_test -O--buildsystem=pybuild
> pybuild --test --test-pytest -i python{version} -p "3.12 3.11"
> I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build;
> python3.12 -m pytest tests
> ============================= test session starts
> ==============================
> platform linux -- Python 3.12.1, pytest-7.4.3, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>
> collected 0 items / 5 errors
>
> ==================================== ERRORS
> ====================================
> _ ERROR collecting
> .pybuild/cpython3_3.12_loompy/build/tests/test_attribute_manager.py _
> ImportError while importing test module
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_attribute_manager.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_attribute_manager.py:3: in <module>
> from loompy import AttributeManager
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E
> --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development
> work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E
> --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was:
> 'cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E
> https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _ ERROR collecting
> .pybuild/cpython3_3.12_loompy/build/tests/test_connection.py _
> ImportError while importing test module
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_connection.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_connection.py:6: in <module>
> import loompy
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E
> --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development
> work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E
> --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was:
> 'cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E
> https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _ ERROR collecting
> .pybuild/cpython3_3.12_loompy/build/tests/test_file_attribute_manager.py _
> ImportError while importing test module
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_file_attribute_manager.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_file_attribute_manager.py:8: in <module>
> from loompy import GlobalAttributeManager
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E
> --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development
> work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E
> --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was:
> 'cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E
> https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ___ ERROR collecting .pybuild/cpython3_3.12_loompy/build/tests/test_main.py
> ____
> ImportError while importing test module
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_main.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_main.py:1: in <module>
> import loompy
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E
> --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development
> work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E
> --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was:
> 'cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E
> https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _ ERROR collecting
> .pybuild/cpython3_3.12_loompy/build/tests/test_validator.py _
> ImportError while importing test module
> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_validator.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_validator.py:6: in <module>
> import loompy
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E
> --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development
> work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E
> --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was:
> 'cannot import name '_typeconv' from 'numba.core.typeconv'
> (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E
> https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> =============================== warnings summary
> ===============================
> loompy/view_manager.py:23
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy/view_manager.py:23:
> SyntaxWarning: "is not" with 'int' literal. Did you mean "!="?
> if type(slice_) is not tuple or len(slice_) is not 2:
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info
> ============================
> ERROR tests/test_attribute_manager.py
> ERROR tests/test_connection.py
> ERROR tests/test_file_attribute_manager.py
> ERROR tests/test_main.py
> ERROR tests/test_validator.py
> !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection
> !!!!!!!!!!!!!!!!!!!!
> ========================= 1 warning, 5 errors in 1.30s
> =========================
> E: pybuild pybuild:395: test: plugin distutils failed with: exit code=2: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build; python3.12 -m pytest
> tests
> I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build;
> python3.11 -m pytest tests
> ============================= test session starts
> ==============================
> platform linux -- Python 3.11.7, pytest-7.4.3, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>
> collected 7 items
>
> tests/test_attribute_manager.py .. [
> 28%]
> tests/test_connection.py . [
> 42%]
> tests/test_file_attribute_manager.py . [
> 57%]
> tests/test_main.py .. [
> 85%]
> tests/test_validator.py .
> [100%]
>
> =============================== warnings summary
> ===============================
> loompy/view_manager.py:23
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy/view_manager.py:23:
> SyntaxWarning: "is not" with a literal. Did you mean "!="?
> if type(slice_) is not tuple or len(slice_) is not 2:
>
> loompy/bus_file.py:67
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy/bus_file.py:67:
> NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied
> to the 'numba.jit' decorator. The implicit default value for this argument is
> currently False, but it will be changed to True in Numba 0.59.0. See
> https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
> for details.[0m
> @jit
>
> loompy/bus_file.py:84
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy/bus_file.py:84:
> NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied
> to the 'numba.jit' decorator. The implicit default value for this argument is
> currently False, but it will be changed to True in Numba 0.59.0. See
> https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
> for details.[0m
> @jit
>
> loompy/bus_file.py:101
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy/bus_file.py:101:
> NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied
> to the 'numba.jit' decorator. The implicit default value for this argument is
> currently False, but it will be changed to True in Numba 0.59.0. See
> https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
> for details.[0m
> @jit
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> ======================== 7 passed, 4 warnings in 2.40s
> =========================
> rm -fr -- /tmp/dh-xdg-rundir-QcowctYQ
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12
> 3.11" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/12/12/python-loompy_3.0.7+dfsg-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20231212;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20231212&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
