Your message dated Wed, 01 Nov 2023 07:07:43 +0000 with message-id <e1qy5kj-000efp...@fasolo.debian.org> and subject line Bug#1042651: fixed in python-pybedtools 0.9.1-1 has caused the Debian Bug report #1042651, regarding python-pybedtools: FTBFS with Sphinx 7.1, docutils 0.20: error: invalid command 'build_sphinx' to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1042651: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1042651 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---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
--- End Message ---
--- Begin Message ---Source: python-pybedtools Source-Version: 0.9.1-1 Done: Lance Lin <lq27...@gmail.com> We believe that the bug you reported is fixed in the latest version of python-pybedtools, 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 1042...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Lance Lin <lq27...@gmail.com> (supplier of updated python-pybedtools package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 27 Oct 2023 19:35:26 +0700 Source: python-pybedtools Architecture: source Version: 0.9.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Lance Lin <lq27...@gmail.com> Closes: 1042651 1048006 Changes: python-pybedtools (0.9.1-1) unstable; urgency=medium . [ Lance Lin ] * Team upload. * New upstream version * d/control: Replace autopkgtest-pkg-python with autopkgtest-pkg-pybuild * d/rules: - Enable build tests - Deselect test_chromsizes test, needs internet - Build docs with sphinx-build for Sphinx 7.1 (Closes: #1042651) - Remove autogenerated files from build * d/python-pybedtools-doc.docs: Change sphinx docs location * d/source/options: Ignore modified source files (Closes: #1048006) * d/patches/yaml_safe_load.patch: Modify safe_load for full_load where needed . [ Andreas Tille ] * Remove unknown files in python module directory * Testsuite: autopkgtest-pkg-python (routine-update) * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * Remove field Testsuite on binary package python-pybedtools-doc that duplicates source. Checksums-Sha1: 2815d5930d6ec7dc9c632cc80b4b4a4f5ebb1844 2520 python-pybedtools_0.9.1-1.dsc 28776b2c1dd94a6dc1c83ac6fb6d8ef7b8393637 12032824 python-pybedtools_0.9.1.orig.tar.xz 7c18bc8f20cb4f2e31146177fd37749c93895a96 29948 python-pybedtools_0.9.1-1.debian.tar.xz 16a192488d347e36d13349b1bdfb794776ef1a32 12633 python-pybedtools_0.9.1-1_amd64.buildinfo Checksums-Sha256: 10830a9f46595c7fa9798250ea5967779ed584e88b9f51d16d7f4c8950dcffe4 2520 python-pybedtools_0.9.1-1.dsc a51c2e3d475677d85af13c8200a1e080fd3408e4336533586038772a56ad500f 12032824 python-pybedtools_0.9.1.orig.tar.xz 1ea148e1e357be412ac419985643d40b65c6e274ba60f9aa8e02c9ce1078bf76 29948 python-pybedtools_0.9.1-1.debian.tar.xz a0ee9a2295ffe6214606ef4206d561effdba0acaa6d2720c71c5719720b01b54 12633 python-pybedtools_0.9.1-1_amd64.buildinfo Files: 20f74b639b426b3904311b90133cf629 2520 python optional python-pybedtools_0.9.1-1.dsc bbaaa1a701513241e8acb0fdb918d9c1 12032824 python optional python-pybedtools_0.9.1.orig.tar.xz e24bc8fbd3871f4b389b0a354cc76adf 29948 python optional python-pybedtools_0.9.1-1.debian.tar.xz 0fe84f6980d867057a4d6860bb51c020 12633 python optional python-pybedtools_0.9.1-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVB9XkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH/Uw//TRpQl3IlpzVu54/8L+u8PxwWtSue6FyR OA5lsD8olAIDgCK26LKlyjwhGKdjTZbRQev1dAdxVf4tcVe9Hts5iXTwP0YkSnGC sQJU8rR1hduNIdldo8Iv9/mWD16x/bsEsdFNziI20cQxx8mVxGD1Mhvr+4WMxfzc TGR28Iom+VJK03tGXijGKxubiL5F2BD2R+JnlOxa6kx2E1xXjka0PDJVS4hGNMbL v0+HSuwTEqTcS6U0CADSZqMV6P3ROdP7x1nNRA2qDeRn2AO+LLfCbodwEGrptnF8 UoHlCw0ZQqKNTOXYLCAvv5AVkwF+3imNP/OZu496VxO8/+xT77aN1dwCQ1c03dhu 2HNRVT9V4VH2leM8EMRpA+wqy2k8g5iK0rMdUOEmh+5ITN70JVzyxb2seATkuSfG qfuSR39tqEyq8yLyVr175dW3tgcmCQheGISi0Y1MAOdBq5AQ45b5bUJW9bQrkxRl SeSEywETGeVP5klc/ko1OCBos3NsN1bgtgEZipjHnxGZovK0M7E4ZxJc2FZay5/w tpuoGOI0dzC0mGti1tpGpjGYJSgscBoUnaKd65dvBL3BoI1uGdGgp7Nz+fc4aLPd jhdJu4K4DelWHVGh1NBc0BrRgJi4a3BoKUMbUufwuqFVDk1ZUMM/N7xZG3Cd6pUS qRZ+VIPyopo= =cQdf -----END PGP SIGNATURE-----
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