Source: python-pybedtools Version: 0.9.0-4 Severity: important Tags: ftbfs User: python-modules-t...@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 sph...@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-t...@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-t...@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