Your message dated Mon, 16 Dec 2024 17:54:07 +0000
with message-id <[email protected]>
and subject line Bug#1090155: fixed in python-pbcore 2.1.2+dfsg-10
has caused the Debian Bug report #1090155,
regarding python-pbcore: FTBFS: ERROR: Invalid value `None` in
intersphinx_mapping['http://docs.python.org/']. Expected a two-element tuple or
list.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1090155: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1090155
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: python-pbcore
Source-Version: 2.1.2+dfsg-10
Done: Andreas Tille <[email protected]>
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 16 Dec 2024 18:22:11 +0100
Source: python-pbcore
Architecture: source
Version: 2.1.2+dfsg-10
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1090155
Changes:
python-pbcore (2.1.2+dfsg-10) unstable; urgency=medium
.
* Remove intersphinx
Closes: #1090155
* d/rules: Fix removal of test remainings
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