Your message dated Tue, 03 Sep 2024 20:59:58 +0000
with message-id <e1slad4-00gi7w...@fasolo.debian.org>
and subject line Bug#1080396: fixed in python-pbcore 2.1.2+dfsg-8
has caused the Debian Bug report #1080396,
regarding python-pbcore: FTBFS: failing tests
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 ow...@bugs.debian.org
immediately.)
--
1080396: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1080396
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: python-pbcore
Source-Version: 2.1.2+dfsg-8
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
python-pbcore, 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 1080...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated python-pbcore
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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 03 Sep 2024 21:57:31 +0200
Source: python-pbcore
Architecture: source
Version: 2.1.2+dfsg-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1080396
Changes:
python-pbcore (2.1.2+dfsg-8) unstable; urgency=medium
.
* d/rules: remove nudge to use setuptools test. (Closes: #1080396)
* d/rules; remove unknown files in Python module directory.
* d/control: declare compliance to standards version 4.7.0.
Checksums-Sha1:
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python-pbcore_2.1.2+dfsg-8.debian.tar.xz
Checksums-Sha256:
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python-pbcore_2.1.2+dfsg-8.dsc
2d46a705cef95ccf2860f6a0b2fc1fee31b0729d06121128385f7358cf22b7c3 60232
python-pbcore_2.1.2+dfsg-8.debian.tar.xz
Files:
5d36ee9bdc103b6949de63841da36522 2804 python optional
python-pbcore_2.1.2+dfsg-8.dsc
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