[Debichem-devel] Bug#1045512: python-pymzml: Fails to build source after successful build

Lucas Nussbaum lucas at debian.org
Sun Aug 13 20:21:16 BST 2023 

Source: python-pymzml
Version: 2.5.2+repack1-1
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-pymzml
> dpkg-buildpackage: info: source version 2.5.2+repack1-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Filippo Rusconi <lopippo at debian.org>
>  dpkg-source --before-build .
>  fakeroot debian/rules clean
> dh clean --with python3 --buildsystem=pybuild
>    dh_auto_clean -O--buildsystem=pybuild
> 	pybuild --clean -i python{version} -p 3.11
> I: pybuild base:275: python3.11 setup.py clean 
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_pymzml/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 -rf .pybuild/
> 	find . -name \*.pyc -exec rm {} \;
>    dh_autoreconf_clean -O--buildsystem=pybuild
> 	rm -f debian/python-pymzml-doc.debhelper.log debian/python3-pymzml.debhelper.log
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> 	rm -f debian/debhelper-build-stamp
> 	rm -rf debian/.debhelper/
> 	rm -f -- debian/python3-pymzml.substvars debian/python3-pymzml.postinst.debhelper debian/python3-pymzml.prerm.debhelper debian/python-pymzml-doc.substvars debian/files
> 	rm -fr -- debian/python3-pymzml/ debian/tmp/ debian/python-pymzml-doc/
> 	find .  \( \( \
> 		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
> 	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
> 		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
> 		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
> 		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
> 		\) -exec rm -f {} + \) -o \
> 		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
> rm -rfv debian/source/include-binaries
> removed 'debian/source/include-binaries'
> rm -rfv "debian/doc"
> removed 'debian/doc/pymzML.pdf'
> removed 'debian/doc/html/.buildinfo'
> removed 'debian/doc/html/suppl_material.html'
> removed 'debian/doc/html/genindex.html'
> removed 'debian/doc/html/modules.html'
> removed 'debian/doc/html/custom_fileclass.html'
> removed 'debian/doc/html/searchindex.js'
> removed 'debian/doc/html/index_gzip.html'
> removed 'debian/doc/html/quick_start.html'
> removed 'debian/doc/html/examples.html'
> removed 'debian/doc/html/pymzml_regex_patterns.html'
> removed 'debian/doc/html/pymzml_spec.html'
> removed 'debian/doc/html/plot.html'
> removed 'debian/doc/html/_modules/plot_chromatogram.html'
> removed 'debian/doc/html/_modules/simple_parser_v2.html'
> removed 'debian/doc/html/_modules/plot_spectrum.html'
> removed 'debian/doc/html/_modules/has_peak.html'
> removed 'debian/doc/html/_modules/gzip_mzml.html'
> removed 'debian/doc/html/_modules/access_run_info.html'
> removed 'debian/doc/html/_modules/extract_ion_chromatogram.html'
> removed 'debian/doc/html/_modules/highest_peaks.html'
> removed 'debian/doc/html/_modules/index.html'
> removed 'debian/doc/html/_modules/deprecation_check.html'
> removed 'debian/doc/html/_modules/get_precursors.html'
> removed 'debian/doc/html/_modules/simple_parser.html'
> removed 'debian/doc/html/_modules/plot_spectrum_with_annotation.html'
> removed 'debian/doc/html/_modules/pymzml/run.html'
> removed 'debian/doc/html/_modules/pymzml/file_classes/standardMzml.html'
> removed 'debian/doc/html/_modules/pymzml/file_classes/indexedGzip.html'
> removed 'debian/doc/html/_modules/pymzml/file_classes/standardGzip.html'
> removed directory 'debian/doc/html/_modules/pymzml/file_classes'
> removed 'debian/doc/html/_modules/pymzml/plot.html'
> removed 'debian/doc/html/_modules/pymzml/file_interface.html'
> removed 'debian/doc/html/_modules/pymzml/utils/GSGR.html'
> removed 'debian/doc/html/_modules/pymzml/utils/GSGW.html'
> removed directory 'debian/doc/html/_modules/pymzml/utils'
> removed 'debian/doc/html/_modules/pymzml/spec.html'
> removed directory 'debian/doc/html/_modules/pymzml'
> removed 'debian/doc/html/_modules/multi_threading_file_compression.html'
> removed 'debian/doc/html/_modules/queryOBO.html'
> removed 'debian/doc/html/_modules/polarity.html'
> removed 'debian/doc/html/_modules/compare_spectra.html'
> removed directory 'debian/doc/html/_modules'
> removed 'debian/doc/html/objects.inv'
> removed 'debian/doc/html/index.html'
> removed 'debian/doc/html/_sources/pymzml_spec.rst.txt'
> removed 'debian/doc/html/_sources/pymzml_run.rst.txt'
> removed 'debian/doc/html/_sources/index.rst.txt'
> removed 'debian/doc/html/_sources/pymzml_utils.rst.txt'
> removed 'debian/doc/html/_sources/custom_fileclass.rst.txt'
> removed 'debian/doc/html/_sources/quick_start.rst.txt'
> removed 'debian/doc/html/_sources/obo.rst.txt'
> removed 'debian/doc/html/_sources/pymzml_regex_patterns.rst.txt'
> removed 'debian/doc/html/_sources/examples.rst.txt'
> removed 'debian/doc/html/_sources/suppl_material.rst.txt'
> removed 'debian/doc/html/_sources/example_scripts.rst.txt'
> removed 'debian/doc/html/_sources/modules.rst.txt'
> removed 'debian/doc/html/_sources/file_handlers.rst.txt'
> removed 'debian/doc/html/_sources/plot.rst.txt'
> removed 'debian/doc/html/_sources/intro.rst.txt'
> removed 'debian/doc/html/_sources/index_gzip.rst.txt'
> removed directory 'debian/doc/html/_sources'
> removed 'debian/doc/html/_static/css/theme.css'
> removed 'debian/doc/html/_static/css/badge_only.css'
> removed directory 'debian/doc/html/_static/css'
> removed 'debian/doc/html/_static/minus.png'
> removed 'debian/doc/html/_static/doctools.js'
> removed 'debian/doc/html/_static/plus.png'
> removed 'debian/doc/html/_static/sphinx_highlight.js'
> removed 'debian/doc/html/_static/jquery.js'
> removed 'debian/doc/html/_static/_sphinx_javascript_frameworks_compat.js'
> removed 'debian/doc/html/_static/language_data.js'
> removed 'debian/doc/html/_static/js/theme.js'
> removed directory 'debian/doc/html/_static/js'
> removed 'debian/doc/html/_static/underscore.js'
> removed 'debian/doc/html/_static/fonts/RobotoSlab-Regular.woff2'
> removed 'debian/doc/html/_static/fonts/fontawesome-webfont.woff2'
> removed 'debian/doc/html/_static/fonts/fontawesome-webfont.ttf'
> removed 'debian/doc/html/_static/fonts/fontawesome-webfont.woff'
> removed 'debian/doc/html/_static/fonts/Lato-Bold.ttf'
> removed 'debian/doc/html/_static/fonts/fontawesome-webfont.svg'
> removed 'debian/doc/html/_static/fonts/Lato-Italic.woff2'
> removed 'debian/doc/html/_static/fonts/Lato-BoldItalic.woff2'
> removed 'debian/doc/html/_static/fonts/Lato-Bold.woff2'
> removed 'debian/doc/html/_static/fonts/fontawesome-webfont.eot'
> removed 'debian/doc/html/_static/fonts/Lato-BoldItalic.ttf'
> removed 'debian/doc/html/_static/fonts/RobotoSlab-Bold.woff2'
> removed 'debian/doc/html/_static/fonts/Lato-Regular.woff2'
> removed 'debian/doc/html/_static/fonts/Lato-Regular.ttf'
> removed 'debian/doc/html/_static/fonts/Lato-Italic.ttf'
> removed directory 'debian/doc/html/_static/fonts'
> removed 'debian/doc/html/_static/file.png'
> removed 'debian/doc/html/_static/basic.css'
> removed 'debian/doc/html/_static/documentation_options.js'
> removed 'debian/doc/html/_static/pygments.css'
> removed 'debian/doc/html/_static/searchtools.js'
> removed directory 'debian/doc/html/_static'
> removed 'debian/doc/html/intro.html'
> removed 'debian/doc/html/pymzml_run.html'
> removed 'debian/doc/html/py-modindex.html'
> removed 'debian/doc/html/pymzml_utils.html'
> removed 'debian/doc/html/file_handlers.html'
> removed 'debian/doc/html/search.html'
> removed 'debian/doc/html/obo.html'
> removed 'debian/doc/html/example_scripts.html'
> removed directory 'debian/doc/html'
> removed directory 'debian/doc'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building python-pymzml using existing ./python-pymzml_2.5.2+repack1.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: file python-pymzml-2.5.2+repack1/pymzml.egg-info/SOURCES.txt has no final newline (either original or modified version)
> dpkg-source: info: local changes detected, the modified files are:
>  python-pymzml-2.5.2+repack1/pymzml.egg-info/PKG-INFO
>  python-pymzml-2.5.2+repack1/pymzml.egg-info/SOURCES.txt
>  python-pymzml-2.5.2+repack1/pymzml.egg-info/dependency_links.txt
>  python-pymzml-2.5.2+repack1/pymzml.egg-info/requires.txt
>  python-pymzml-2.5.2+repack1/pymzml.egg-info/top_level.txt
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/python-pymzml_2.5.2+repack1-1.diff.FWwYKS
> dpkg-source: info: Hint: make sure the version in debian/changelog matches the unpacked source tree
> dpkg-source: info: you can integrate the local changes with dpkg-source --commit
> dpkg-buildpackage: error: dpkg-source -b . subprocess returned exit status 2
> 
> 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-pymzml_2.5.2+repack1-1_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.

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