Your message dated Wed, 08 Nov 2023 10:05:43 +0000
with message-id <[email protected]>
and subject line Bug#1047165: fixed in python-pysam 0.22.0+ds-1
has caused the Debian Bug report #1047165,
regarding python-pysam: Fails to build source after successful build
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.
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--
1047165: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1047165
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: python-pysam
Version: 0.21.0+ds-1
Severity: minor
Tags: trixie sid ftbfs
User: [email protected]
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: [email protected]
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 Ãtienne Mollier
> <[email protected]>
> 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.
--- End Message ---
--- Begin Message ---
Source: python-pysam
Source-Version: 0.22.0+ds-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-pysam, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated python-pysam package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 08 Nov 2023 10:23:13 +0100
Source: python-pysam
Architecture: source
Version: 0.22.0+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1047165 1055505
Changes:
python-pysam (0.22.0+ds-1) unstable; urgency=medium
.
* New upstream version
Closes: #1055505
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* Fix clean target
Closes: #1047165
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