[Debian-med-packaging] Bug#1080396: python-pbcore: FTBFS: failing tests
Santiago Vila
sanvila at debian.org
Tue Sep 3 11:57:24 BST 2024
Package: src:python-pbcore
Version: 2.1.2+dfsg-7
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
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
I: pybuild base:311: python3.12 setup.py config
/usr/lib/python3/dist-packages/setuptools/dist.py:450: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
By 2024-Sep-26, 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.warn_dash_deprecation(opt, section)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
running config
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:311: /usr/bin/python3 setup.py build
/usr/lib/python3/dist-packages/setuptools/dist.py:450: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
By 2024-Sep-26, 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.warn_dash_deprecation(opt, section)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore
copying pbcore/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore
copying pbcore/sequence.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/model
copying pbcore/model/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/model
copying pbcore/model/baseRegions.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/model
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/FastqIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/base.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/GffIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/opener.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/FastaIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/_utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/VcfIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/FofnIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry
copying pbcore/chemistry/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry
copying pbcore/chemistry/chemistry.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/util
copying pbcore/util/statistics.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/util
copying pbcore/util/decorators.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/util
copying pbcore/util/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/util
copying pbcore/util/ToolRunner.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/util
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetErrors.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/run_split.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetMetaTypes.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetReader.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetUtils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetValidator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetMembers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetWriter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align
copying pbcore/io/align/BamAlignment.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align
copying pbcore/io/align/BlasrIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align
copying pbcore/io/align/PacBioBamIndex.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align
copying pbcore/io/align/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align
copying pbcore/io/align/BamIO.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align
copying pbcore/io/align/_BamSupport.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align
copying pbcore/io/align/_AlignmentMixin.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/align
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
running egg_info
creating pbcore.egg-info
writing pbcore.egg-info/PKG-INFO
writing dependency_links to pbcore.egg-info/dependency_links.txt
writing entry points to pbcore.egg-info/entry_points.txt
writing requirements to pbcore.egg-info/requires.txt
writing top-level names to pbcore.egg-info/top_level.txt
writing manifest file 'pbcore.egg-info/SOURCES.txt'
reading manifest file 'pbcore.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching '*.txt'
warning: no directories found matching 'bin'
adding license file 'LICENSE'
writing manifest file 'pbcore.egg-info/SOURCES.txt'
/usr/lib/python3/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'pbcore.chemistry.resources' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'pbcore.chemistry.resources' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'pbcore.chemistry.resources' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'pbcore.chemistry.resources' to be distributed and are
already explicitly excluding 'pbcore.chemistry.resources' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry/resources
copying pbcore/chemistry/resources/mapping.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/chemistry/resources
copying pbcore/data/Fluidigm_human_amplicons.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/Fluidigm_human_amplicons.fasta.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/Fluidigm_human_amplicons_tiny.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/barcodes-ed65-450.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/barcodes-ed65-450.fasta.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/blasr-output.m4 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/blasr-output.m5 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/chemistry.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/empty.aligned_subreads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/empty.aligned_subreads.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/empty.ccs.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/empty.ccs.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/empty2.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/empty2.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/lambdaNEB.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/lambdaNEB.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/variants.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/weird.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/weird.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
copying pbcore/data/datasets/CollectionMetadata.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/alignment.dataset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/barcode.dataset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/ccsaligned.dataset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/ccsread.dataset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/contig.dataset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/empty_lambda.aligned.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/empty_lambda.aligned.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/empty_lambda.aligned.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/fofn.fofn -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/lambda.alignmentset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/lambda.referenceset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim.alignmentset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.alignmentset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.pbalign.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.reference.fasta -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.reference.fasta.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.referenceset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.subreads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.subreads.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.subreadset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.alignmentset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.pbalign.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.subreads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.subreads.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.subreadset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/reference.dataset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/subread.dataset.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/subreadSetWithStats.xml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data/datasets
PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build /usr/bin/make doc
make[2]: Entering directory '/<<PKGBUILDDIR>>'
sphinx-apidoc -o doc/ pbcore/ && cd doc/ && make html
make[3]: Entering directory '/<<PKGBUILDDIR>>/doc'
sphinx-apidoc -o . -d 4 ../pbcore/
sphinx-build -b html -d _build/doctrees . _build/html
Running Sphinx v7.4.7
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
WARNING: The pre-Sphinx 1.0 'intersphinx_mapping' format is deprecated and will be removed in Sphinx 8. Update to the current format as described in the documentation. Hint: `intersphinx_mapping = {'<name>': ('http://docs.python.org/', None)}`.https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#confval-intersphinx_mapping
loading intersphinx inventory 'main_inventory' from http://docs.python.org/objects.inv...
intersphinx inventory has moved: http://docs.python.org/objects.inv -> https://docs.python.org/3/objects.inv
building [mo]: targets for 0 po files that are out of date
writing output...
building [html]: targets for 11 source files that are out of date
updating environment: [new config] 11 added, 0 changed, 0 removed
reading sources... [ 9%] index
reading sources... [ 18%] modules
reading sources... [ 27%] pbcore
reading sources... [ 36%] pbcore.chemistry
reading sources... [ 45%] pbcore.data
reading sources... [ 55%] pbcore.data.datasets
reading sources... [ 64%] pbcore.io
reading sources... [ 73%] pbcore.io.align
reading sources... [ 82%] pbcore.io.dataset
reading sources... [ 91%] pbcore.model
reading sources... [100%] pbcore.util
/<<PKGBUILDDIR>>/doc/pbcore.rst:7: WARNING: toctree contains reference to nonexisting document 'pbcore.deprecated'
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io/dataset/DataSetMembers.py:docstring of pbcore.io.dataset.DataSetMembers:47: ERROR: Unexpected indentation.
WARNING: autodoc: failed to import module 'Process' from module 'pbcore.util'; the following exception was raised:
No module named 'pbcore.util.Process'
looking for now-outdated files... none found
pickling environment... done
checking consistency... /<<PKGBUILDDIR>>/doc/modules.rst: WARNING: document isn't included in any toctree
/<<PKGBUILDDIR>>/doc/pbcore.data.datasets.rst: WARNING: document isn't included in any toctree
/<<PKGBUILDDIR>>/doc/pbcore.io.align.rst: WARNING: document isn't included in any toctree
/<<PKGBUILDDIR>>/doc/pbcore.io.dataset.rst: WARNING: document isn't included in any toctree
done
preparing documents... done
copying assets...
copying static files... done
copying extra files... done
copying assets: done
writing output... [ 9%] index
writing output... [ 18%] modules
writing output... [ 27%] pbcore
writing output... [ 36%] pbcore.chemistry
writing output... [ 45%] pbcore.data
writing output... [ 55%] pbcore.data.datasets
writing output... [ 64%] pbcore.io
writing output... [ 73%] pbcore.io.align
writing output... [ 82%] pbcore.io.dataset
writing output... [ 91%] pbcore.model
writing output... [100%] pbcore.util
WARNING: dot command 'dot' cannot be run (needed for graphviz output), check the graphviz_dot setting
generating indices... genindex py-modindex done
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 9 warnings.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# we need to exclude tests requiring pbtestdata which is not packaged
mkdir -p /tmp/tests_avoid
mv `grep -l pbtestdata tests/*.py` /tmp/tests_avoid
# for whatever reason this test is failing as well - just skip it for the moment
mv tests/test_pbdataset_filters.py /tmp/tests_avoid
PYBUILD_SYSTEM=custom \
PYBUILD_TEST_ARGS="{interpreter} setup.py test" \
dh_auto_test
I: pybuild base:311: python3.12 setup.py test
/usr/lib/python3/dist-packages/setuptools/dist.py:450: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
By 2024-Sep-26, 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.warn_dash_deprecation(opt, section)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:268: UserWarning: Unknown distribution option: 'tests_require'
warnings.warn(msg)
/usr/lib/python3/dist-packages/ptr.py:38: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated.
!!
********************************************************************************
Please remove any references to `setuptools.command.test` in all supported versions of the affected package.
By 2024-Nov-15, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
********************************************************************************
!!
class PyTest(orig.test):
running pytest
/usr/lib/python3/dist-packages/setuptools/dist.py:450: SetuptoolsDeprecationWarning: Invalid dash-separated options
!!
********************************************************************************
Usage of dash-separated 'description-file' will not be supported in future
versions. Please use the underscore name 'description_file' instead.
By 2024-Sep-26, 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.warn_dash_deprecation(opt, section)
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!
********************************************************************************
Please avoid running ``setup.py`` and ``easy_install``.
Instead, use pypa/build, pypa/installer or other
standards-based tools.
See https://github.com/pypa/setuptools/issues/917 for details.
********************************************************************************
!!
self.initialize_options()
/usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: 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()
/usr/lib/python3/dist-packages/ptr.py:132: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated.
!!
********************************************************************************
Please remove any references to `setuptools.command.test` in all supported versions of the affected package.
By 2024-Nov-15, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
********************************************************************************
!!
if hasattr(orig.test, 'install_dists'):
/usr/lib/python3/dist-packages/ptr.py:90: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated.
!!
********************************************************************************
Please remove any references to `setuptools.command.test` in all supported versions of the affected package.
By 2024-Nov-15, you need to update your project and remove deprecated calls
or your builds will no longer be supported.
********************************************************************************
!!
i_d = getattr(orig.test, 'install_dists', self._install_dists_compat)
/usr/lib/python3/dist-packages/ptr.py:82: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
!!
********************************************************************************
Requirements should be satisfied by a PEP 517 installer.
If you are using pip, you can try `pip install --use-pep517`.
********************************************************************************
!!
ir_d = dist.fetch_build_eggs(dist.install_requires or [])
Traceback (most recent call last):
File "/<<PKGBUILDDIR>>/setup.py", line 16, in <module>
setup(
File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 111, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 184, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/setuptools/_distutils/core.py", line 200, in run_commands
dist.run_commands()
File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 964, in run_commands
self.run_command(cmd)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 948, in run_command
super().run_command(command)
File "/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py", line 983, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/ptr.py", line 150, in run
self._super_run()
File "/usr/lib/python3/dist-packages/ptr.py", line 136, in _super_run
installed_dists = self.install_dists(self.distribution)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/ptr.py", line 91, in install_dists
return _itertools.chain(i_d(dist), self.install_extra_dists(dist))
^^^^^^^^^
File "/usr/lib/python3/dist-packages/ptr.py", line 83, in _install_dists_compat
tr_d = dist.fetch_build_eggs(dist.tests_require or [])
^^^^^^^^^^^^^^^^^^
AttributeError: 'Distribution' object has no attribute 'tests_require'. Did you mean: 'extras_require'?
E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: python3.12 setup.py test
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 returned exit code 13
make[1]: *** [debian/rules:34: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:13: 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/202409/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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