[Debian-med-packaging] Bug#1042651: python-pybedtools: FTBFS with Sphinx 7.1, docutils 0.20: error: invalid command 'build_sphinx'
Lucas Nussbaum
lucas at debian.org
Sun Jul 30 19:24:29 BST 2023
Source: python-pybedtools
Version: 0.9.0-4
Severity: important
Tags: ftbfs
User: python-modules-team at lists.alioth.debian.org
Usertags: sphinx7.1
Hi,
python-pybedtools fails to build with Sphinx 7.1 and docutils 0.20, both of which
are currently available in experimental.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> python3 setup.py cythonize
> /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
> if not hasattr(numpy, method):
> /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
> obj = getattr(themodule, elem)
> running cythonize
> /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/pybedtools/cbedtools.pxd
> tree = Parsing.p_module(s, pxd, full_module_name)
> /usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /<<PKGBUILDDIR>>/pybedtools/featurefuncs.pyx
> tree = Parsing.p_module(s, pxd, full_module_name)
> Compiling pybedtools/cbedtools.pyx because it changed.
> Compiling pybedtools/featurefuncs.pyx because it changed.
> [1/2] Cythonizing pybedtools/cbedtools.pyx
> [2/2] Cythonizing pybedtools/featurefuncs.pyx
> dh_auto_build
> I: pybuild base:240: /usr/bin/python3 setup.py build
> /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
> if not hasattr(numpy, method):
> /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
> obj = getattr(themodule, elem)
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/genome_registry.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/bedtool.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/paths.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/helpers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/filenames.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/settings.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/logger.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/stats.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/parallel.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_contrib.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_gzip_support.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/tfuncs.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_len_leak.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_issues.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_iter.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_cbedtools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_1.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_pathlib.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_helpers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/regression_tests.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/genomepy_integration.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
> copying pybedtools/contrib/long_range_interaction.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
> copying pybedtools/contrib/bigwig.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
> copying pybedtools/contrib/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
> copying pybedtools/contrib/plotting.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
> copying pybedtools/contrib/intersection_matrix.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
> copying pybedtools/contrib/venn_maker.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
> copying pybedtools/contrib/bigbed.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/contrib
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> running egg_info
> creating pybedtools.egg-info
> writing pybedtools.egg-info/PKG-INFO
> writing dependency_links to pybedtools.egg-info/dependency_links.txt
> writing requirements to pybedtools.egg-info/requires.txt
> writing top-level names to pybedtools.egg-info/top_level.txt
> writing manifest file 'pybedtools.egg-info/SOURCES.txt'
> reading manifest file 'pybedtools.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no files found matching '*.c' under directory 'pybedtools'
> warning: no previously-included files matching '__pycache__' found under directory '*'
> warning: no previously-included files matching '*.py[co]' found under directory '*'
> adding license file 'LICENSE.txt'
> writing manifest file 'pybedtools.egg-info/SOURCES.txt'
> /usr/lib/python3/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'pybedtools.include' is absent from the `packages` configuration.
> !!
>
> ********************************************************************************
> ############################
> # Package would be ignored #
> ############################
> Python recognizes 'pybedtools.include' 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 'pybedtools.include' 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 'pybedtools.include' to be distributed and are
> already explicitly excluding 'pybedtools.include' 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)
> copying pybedtools/_Window.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/cbedtools.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/cbedtools.pxd -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/cbedtools.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/featurefuncs.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> copying pybedtools/featurefuncs.pyx -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
> copying pybedtools/include/bedFile.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
> copying pybedtools/include/bedFile.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
> copying pybedtools/include/fileType.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
> copying pybedtools/include/fileType.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
> copying pybedtools/include/gzstream.cpp -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
> copying pybedtools/include/gzstream.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
> copying pybedtools/include/lineFileUtilities.h -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/include
> copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/test_peaks.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/venn.c.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.50.200.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/reads.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.cram -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/m1.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/multibamcov_test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/exons.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.sorted.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/1000genomes-example.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/small.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/a.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/tag_test1.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/issue319.out.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/v.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/hg19.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/c.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/democonfig.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/y.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.1.100.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/venn.b.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/b.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/issue_121.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/issue319.vcf.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/issue319.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/bedpe2.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/a.links.html -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.1.100.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/test_bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/vcf-stderr-test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/vcf-stderr-test.vcf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/test.fa.fai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/mm9.bed12 -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/expand_test.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/small.fastq -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.othersort.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/tag_test2.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/hg38-problem.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/genome.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/d.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.sorted.bam.bai -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/test_tsses.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/a.igv_script -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/test.fa -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/snps.bed.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/hg38-base.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.50.200.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/164.gtf -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/gdc.gff -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/x.bam -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/bedpe.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/data/x.bed -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test/data
> copying pybedtools/test/gchart-expected.png -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/mpl-expected.png -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/prevent_open_file_regression -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_cases.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_merge215.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_merge227.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_shuffle215.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> copying pybedtools/test/test_shuffle227.yaml -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/test
> running build_ext
> building 'pybedtools.cbedtools' extension
> INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
>
> creating build
> creating build/temp.linux-x86_64-cpython-311
> creating build/temp.linux-x86_64-cpython-311/pybedtools
> creating build/temp.linux-x86_64-cpython-311/pybedtools/include
> INFO: compile options: '-Ipybedtools/include/ -I/usr/include/python3.11 -c'
> INFO: x86_64-linux-gnu-gcc: pybedtools/cbedtools.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/bedFile.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/fileType.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/gzstream.cpp
> In file included from pybedtools/include/bedFile.cpp:12:
> pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
> pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 92 | for (register short i = 0; i < _binLevels; ++i) {
> | ^
> In file included from pybedtools/cbedtools.cpp:802:
> pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
> pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 92 | for (register short i = 0; i < _binLevels; ++i) {
> | ^
> INFO: x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-311/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-311/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/cbedtools.cpython-311-x86_64-linux-gnu.so
> building 'pybedtools.featurefuncs' extension
> INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
>
> INFO: compile options: '-Ipybedtools/include/ -I/usr/include/python3.11 -c'
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/bedFile.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/fileType.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/gzstream.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/featurefuncs.cpp
> In file included from pybedtools/include/bedFile.cpp:12:
> pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
> pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 92 | for (register short i = 0; i < _binLevels; ++i) {
> | ^
> In file included from pybedtools/featurefuncs.cpp:802:
> pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
> pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 92 | for (register short i = 0; i < _binLevels; ++i) {
> | ^
> INFO: x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-311/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-311/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pybedtools/build/pybedtools/featurefuncs.cpython-311-x86_64-linux-gnu.so
> python3 setup.py develop --user
> /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
> if not hasattr(numpy, method):
> /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
> obj = getattr(themodule, elem)
> running develop
> /usr/lib/python3/dist-packages/setuptools/command/develop.py:40: 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.
> ********************************************************************************
>
> !!
> easy_install.initialize_options(self)
> /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()
> running egg_info
> writing pybedtools.egg-info/PKG-INFO
> writing dependency_links to pybedtools.egg-info/dependency_links.txt
> writing requirements to pybedtools.egg-info/requires.txt
> writing top-level names to pybedtools.egg-info/top_level.txt
> reading manifest file 'pybedtools.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> warning: no files found matching '*.c' under directory 'pybedtools'
> warning: no previously-included files matching '__pycache__' found under directory '*'
> warning: no previously-included files matching '*.py[co]' found under directory '*'
> adding license file 'LICENSE.txt'
> writing manifest file 'pybedtools.egg-info/SOURCES.txt'
> running build_ext
> building 'pybedtools.cbedtools' extension
> INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
>
> INFO: compile options: '-Ipybedtools/include/ -I/usr/include/python3.11 -c'
> INFO: x86_64-linux-gnu-gcc: pybedtools/cbedtools.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/bedFile.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/fileType.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/gzstream.cpp
> In file included from pybedtools/include/bedFile.cpp:12:
> pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
> pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 92 | for (register short i = 0; i < _binLevels; ++i) {
> | ^
> In file included from pybedtools/cbedtools.cpp:802:
> pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
> pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 92 | for (register short i = 0; i < _binLevels; ++i) {
> | ^
> INFO: x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pybedtools/cbedtools.o build/temp.linux-x86_64-cpython-311/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-311/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/pybedtools/cbedtools.cpython-311-x86_64-linux-gnu.so
> building 'pybedtools.featurefuncs' extension
> INFO: C compiler: x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
>
> INFO: compile options: '-Ipybedtools/include/ -I/usr/include/python3.11 -c'
> INFO: x86_64-linux-gnu-gcc: pybedtools/featurefuncs.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/bedFile.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/gzstream.cpp
> INFO: x86_64-linux-gnu-gcc: pybedtools/include/fileType.cpp
> In file included from pybedtools/include/bedFile.cpp:12:
> pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
> pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 92 | for (register short i = 0; i < _binLevels; ++i) {
> | ^
> In file included from pybedtools/featurefuncs.cpp:802:
> pybedtools/include/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
> pybedtools/include/bedFile.h:92:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
> 92 | for (register short i = 0; i < _binLevels; ++i) {
> | ^
> INFO: x86_64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/pybedtools/featurefuncs.o build/temp.linux-x86_64-cpython-311/pybedtools/include/bedFile.o build/temp.linux-x86_64-cpython-311/pybedtools/include/fileType.o build/temp.linux-x86_64-cpython-311/pybedtools/include/gzstream.o -L/usr/lib/x86_64-linux-gnu -lstdc++ -lz -o /<<PKGBUILDDIR>>/pybedtools/featurefuncs.cpython-311-x86_64-linux-gnu.so
> Creating /<<PKGBUILDDIR>>/fakehome/.local/lib/python3.11/site-packages/pybedtools.egg-link (link to .)
> Adding pybedtools 0.9.0 to easy-install.pth file
>
> Installed /<<PKGBUILDDIR>>
> Processing dependencies for pybedtools==0.9.0
> Searching for six==1.16.0
> Best match: six 1.16.0
> Adding six 1.16.0 to easy-install.pth file
>
> Using /usr/lib/python3/dist-packages
> Searching for pysam==0.21.0
> Best match: pysam 0.21.0
> Adding pysam 0.21.0 to easy-install.pth file
>
> Using /usr/lib/python3/dist-packages
> Finished processing dependencies for pybedtools==0.9.0
> python3 setup.py build_sphinx
> /usr/lib/python3/dist-packages/pythran/tables.py:4530: FutureWarning: In the future `np.bool` will be defined as the corresponding NumPy scalar.
> if not hasattr(numpy, method):
> /usr/lib/python3/dist-packages/pythran/tables.py:4563: FutureWarning: In the future `np.bytes` will be defined as the corresponding NumPy scalar.
> obj = getattr(themodule, elem)
> usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
> or: setup.py --help [cmd1 cmd2 ...]
> or: setup.py --help-commands
> or: setup.py cmd --help
>
> error: invalid command 'build_sphinx'
> make[1]: *** [debian/rules:23: override_dh_auto_build] Error 1
The full build log is available from:
http://qa-logs.debian.net/2023/07/30/exp/python-pybedtools_0.9.0-4_unstable_sphinx-exp.log
Please see [1] for Sphinx changelog and [2] for Docutils changelog.
Also see [3] for the list of deprecated/removed APIs in Sphinx and possible
alternatives to them.
Some notable changes in Sphinx 6 and Sphinx 7:
- Sphinx no longer includes jquery.js and underscore.js by default.
Please use python3-sphinxcontrib.jquery package if you are using a custom
template and it still needs jquery.
- The setup.py build_sphinx command was removed. Please instead call
sphinx-build or "python3 -m sphinx" directly.
- For packages using the extlinks extension, the caption should contain
exactly one "%s" placeholder (if caption is not None).
In case you have questions, please Cc sphinx at packages.debian.org on reply.
[1]: https://www.sphinx-doc.org/en/master/changes.html
[2]: https://repo.or.cz/docutils.git/blob/refs/tags/docutils-0.20.1:/RELEASE-NOTES.txt
[3]: https://www.sphinx-doc.org/en/master/extdev/deprecated.html#dev-deprecated-apis
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=sphinx7.1;users=python-modules-team@lists.alioth.debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=sphinx7.1&fusertaguser=python-modules-team@lists.alioth.debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
More information about the Debian-med-packaging
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