Package: src:python-pbcore
Version: 2.1.2+dfsg-9
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: python3.13 setup.py config
/usr/lib/python3/dist-packages/setuptools/dist.py:491:
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 2025-Mar-03, 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:261: UserWarning:
Unknown distribution option: 'tests_require'
warnings.warn(msg)
running config
I: pybuild base:311: python3.12 setup.py config
/usr/lib/python3/dist-packages/setuptools/dist.py:491:
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 2025-Mar-03, 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:261: 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/python3.13 setup.py build
/usr/lib/python3/dist-packages/setuptools/dist.py:491:
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 2025-Mar-03, 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:261: UserWarning:
Unknown distribution option: 'tests_require'
warnings.warn(msg)
running build
running build_py
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore
copying pbcore/sequence.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore
copying pbcore/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/chemistry
copying pbcore/chemistry/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/chemistry
copying pbcore/chemistry/chemistry.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/chemistry
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/model
copying pbcore/model/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/model
copying pbcore/model/baseRegions.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/model
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/opener.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/VcfIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/FastqIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/FofnIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/_utils.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/base.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/GffIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
copying pbcore/io/FastaIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/util
copying pbcore/util/ToolRunner.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/util
copying pbcore/util/statistics.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/util
copying pbcore/util/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/util
copying pbcore/util/decorators.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/util
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetReader.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetValidator.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetWriter.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetMembers.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/utils.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetUtils.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/run_split.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetErrors.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
copying pbcore/io/dataset/DataSetMetaTypes.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align
copying pbcore/io/align/BamIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align
copying pbcore/io/align/_AlignmentMixin.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align
copying pbcore/io/align/PacBioBamIndex.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align
copying pbcore/io/align/BlasrIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align
copying pbcore/io/align/_BamSupport.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align
copying pbcore/io/align/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align
copying pbcore/io/align/BamAlignment.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align
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_3.13_pbcore/build/pbcore/chemistry/resources
copying pbcore/chemistry/resources/mapping.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/chemistry/resources
copying pbcore/data/Fluidigm_human_amplicons.fasta ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/Fluidigm_human_amplicons.fasta.fai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/Fluidigm_human_amplicons_tiny.fasta ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/barcodes-ed65-450.fasta ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/barcodes-ed65-450.fasta.fai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/blasr-output.m4 ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/blasr-output.m5 ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/chemistry.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/empty.aligned_subreads.bam ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/empty.aligned_subreads.bam.pbi ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/empty.ccs.bam ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/empty.ccs.bam.pbi ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/empty2.bam ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/empty2.bam.pbi ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/lambdaNEB.fa ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/lambdaNEB.fa.fai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying
pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/variants.gff ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/weird.fa ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/weird.fa.fai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data
copying pbcore/data/datasets/CollectionMetadata.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/alignment.dataset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/barcode.dataset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/ccsaligned.dataset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/ccsread.dataset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/contig.dataset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/empty_lambda.aligned.bam ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/empty_lambda.aligned.bam.bai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/empty_lambda.aligned.bam.pbi ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/fofn.fofn ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/lambda.alignmentset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/lambda.referenceset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying
pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying
pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying
pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying
pbcore/data/datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml
-> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim.alignmentset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.alignmentset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.pbalign.bam ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.reference.fasta ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.reference.fasta.fai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.referenceset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.subreads.bam ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.subreads.bam.bai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim0.subreadset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.alignmentset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.pbalign.bam ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.subreads.bam ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.subreads.bam.bai ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/pbalchemysim1.subreadset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/reference.dataset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/subread.dataset.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
copying pbcore/data/datasets/subreadSetWithStats.xml ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_pbcore/build/pbcore/data/datasets
I: pybuild base:311: /usr/bin/python3 setup.py build
/usr/lib/python3/dist-packages/setuptools/dist.py:491:
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 2025-Mar-03, 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:261: 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/sequence.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore
copying pbcore/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore
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/data
copying pbcore/data/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/data
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/opener.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/FastqIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
copying pbcore/io/FofnIO.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/__init__.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/FastaIO.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/io
creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/util
copying pbcore/util/ToolRunner.py ->
/<<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/__init__.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/util
copying pbcore/util/decorators.py ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pbcore/build/pbcore/util
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
creating /<<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/DataSetValidator.py ->
/<<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/DataSetWriter.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/utils.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/__init__.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/DataSetErrors.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
creating /<<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/_AlignmentMixin.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/BlasrIO.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/__init__.py ->
/<<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
running 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
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 v8.1.3
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst':
'restructuredtext'}`.
ERROR: Invalid value `None` in intersphinx_mapping['http://docs.python.org/'].
Expected a two-element tuple or list.
Configuration error:
Invalid `intersphinx_mapping` configuration (1 error).
make[3]: *** [Makefile:48: html] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc'
make[2]: *** [Makefile:32: doc] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [debian/rules:17: override_dh_auto_build] Error 2
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/202412/
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 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.
