[Debian-med-packaging] Bug#1047165: python-pysam: Fails to build source after successful build

Sun Aug 13 20:21:17 BST 2023

Source: python-pysam
Version: 0.21.0+ds-1
Severity: minor
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian-qa at lists.debian.org
Usertags: qa-doublebuild

Hi,

This package fails to build a source package after a successful build
(dpkg-buildpackage ; dpkg-buildpackage -S).

This is probably a clear violation of Debian Policy section 4.9 (clean target),
but this is filed as severity:minor for now, because a discussion on
debian-devel showed that we might want to revisit the requirement of a working
'clean' target.

More information about this class of issues, included common problems and
solutions, is available at
https://wiki.debian.org/qa.debian.org/FTBFS/SourceAfterBuild

Relevant part of the build log:
> cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S
> -----------------------------------------------------------------------------------------------------------------------------------
> 
> dpkg-buildpackage: info: source package python-pysam
> dpkg-buildpackage: info: source version 0.21.0+ds-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Ã‰tienne Mollier <emollier at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> cd tests/pysam_data && /usr/bin/make clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>/tests/pysam_data'
> rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \
> all.stamp *~ calDepth *.dSYM pysam_*.sam \
> ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \
> with_md.sam.gz \
> *.fq.gz
> make[1]: Leaving directory '/<<PKGBUILDDIR>>/tests/pysam_data'
> cd tests/cbcf_data && /usr/bin/make clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
> rm -f all.stamp *.gz *.tbi *.csi *.bcf
> make[1]: Leaving directory '/<<PKGBUILDDIR>>/tests/cbcf_data'
> find . -name "*.pyc" -delete
> find . -name "*.pyxbldc" -delete
> find . -name "tmp_*.bam" -delete
> find . -name "*.bai*" -delete
> find . -name "*.cram*" -delete
> find . -name "pysam_uncompressed.bam" -delete
> rm -rf	tests/pysam_test_work \
> 	tests/example_htslib.gtf.gz.tbi \
> 	tests/log.txt \
> 	tests/test.bam \
> 	tests/_compile_test.c \
> 	tests/pysam_ex2.sam \
> 	tests/__pycache__ \
> 	pysam/calignmentfile.c \
> 	pysam/cbcf.c \
> 	tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
> 	tests/pysam_data/ex1.fa.gz \
> 	tests/pysam_data/ex1.fa.gz.gzi \
> 	tests/pysam_data/ex1_csi.bam.csi
> rm -rf .pytest_cache/
> dh clean --with python3 --buildsystem=pybuild
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> I: pybuild base:275: python3.11 setup.py clean 
> # pysam: cython is available - using cythonize if necessary
> # pysam: htslib mode is external
> # pysam: HTSLIB_CONFIGURE_OPTIONS=None
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pysam/build' (and everything under it)
> 'build/bdist.linux-x86_64' does not exist -- can't clean it
> 'build/scripts-3.11' does not exist -- can't clean it
> rm -f \
> 	pysam/config.py \
> 	pysam/config.h \
> 	pysam/lib*.c \
> 	samtools/config.h \
> 	bcftools/config.h
> rm -rf pysam.egg-info
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    dh_clean -O--buildsystem=pybuild
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building python-pysam using existing ./python-pysam_0.21.0+ds.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to tests/pysam_data/MM-chebi.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/MM-chebi.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/MM-double.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/MM-double.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/MM-multi.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/MM-multi.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/MM-orient.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/MM-orient.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/empty.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/empty.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex1.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex1.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex10.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex10.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex1_csi.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex1_csi.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex2.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex2.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex2_corrupt.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex2_corrupt.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex2_truncated.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex2_truncated.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex3.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex3.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex4.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex4.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex5.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex5.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex6.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex6.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex8.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex8.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex9_fail.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex9_fail.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex9_nofail.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex9_nofail.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/ex_spliced.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/ex_spliced.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/example_aligned_pairs.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/example_aligned_pairs.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/example_bai.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/example_bai.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/example_btag.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/example_btag.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/example_dash_in_chr.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/example_dash_in_chr.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/example_empty_header.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/example_empty_header.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/example_empty_with_header.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/example_empty_with_header.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/example_reverse_complement.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/example_reverse_complement.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/example_unmapped_reads_no_sq.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/example_unmapped_reads_no_sq.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/explicit_index.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/explicit_index.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/issue100.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/issue100.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/rg_with_tab.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/rg_with_tab.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/softclip.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/softclip.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/tag_bug.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/tag_bug.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/test_mapped_unmapped.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/test_mapped_unmapped.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/test_query_position.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/test_query_position.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/test_unaligned.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/test_unaligned.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/uncompressed.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/uncompressed.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to tests/pysam_data/with_md.bam: binary file contents changed
> dpkg-source: error: add tests/pysam_data/with_md.bam in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: unrepresentable changes to source
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 1
> 
> E: Command 'cd /<<PKGBUILDDIR>> && runuser -u user42 -- dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -S' failed to run.

The full build log is available from:
http://qa-logs.debian.net/2023/08/13/python-pysam_0.21.0+ds-1_unstable.log

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.