Bug#1043609: cctbx: Fails to build source after successful build

[Lucas Nussbaum]

Source: cctbx
Version: 2022.9+ds2+~3.11.2+ds1-6
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 cctbx
> dpkg-buildpackage: info: source version 2022.9+ds2+~3.11.2+ds1-6
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Stefano Rivera <stefanor at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --buildsystem=pybuild
> 	rm -f debian/libcctbx-dev.debhelper.log debian/libcctbx0.debhelper.log debian/python3-cctbx.debhelper.log
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_clean
> 	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/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 {} \;
> find . -name __pycache__ -type d -exec rm -rf {} \;
> rm -f setup.py
> rm -rf annlib annlib_adaptbx
> rm -rf ccp4io ccp4io_adaptbx
> rm -rf gui_resources
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    dh_clean -O--buildsystem=pybuild
> 	rm -f debian/debhelper-build-stamp
> 	rm -rf debian/.debhelper/
> 	rm -f -- debian/libcctbx0.substvars debian/libcctbx-dev.substvars debian/python3-cctbx.substvars debian/python3-cctbx.postinst.debhelper debian/python3-cctbx.prerm.debhelper debian/files
> 	rm -fr -- debian/libcctbx0/ debian/tmp/ debian/libcctbx-dev/ debian/python3-cctbx/
> 	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 \
> 		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building cctbx using existing ./cctbx_2022.9+ds2+~3.11.2+ds1.orig-dxtbx.tar.xz
> dpkg-source: info: building cctbx using existing ./cctbx_2022.9+ds2+~3.11.2+ds1.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: ignoring deletion of file dox/Doxyfile.orig, use --include-removal to override
> dpkg-source: warning: file cctbx-2022.9+ds2+~3.11.2+ds1/cctbx.egg-info/SOURCES.txt has no final newline (either original or modified version)
> dpkg-source: warning: file cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx.egg-info/SOURCES.txt has no final newline (either original or modified version)
> dpkg-source: info: local changes detected, the modified files are:
>  cctbx-2022.9+ds2+~3.11.2+ds1/cctbx.egg-info/PKG-INFO
>  cctbx-2022.9+ds2+~3.11.2+ds1/cctbx.egg-info/SOURCES.txt
>  cctbx-2022.9+ds2+~3.11.2+ds1/cctbx.egg-info/dependency_links.txt
>  cctbx-2022.9+ds2+~3.11.2+ds1/cctbx.egg-info/requires.txt
>  cctbx-2022.9+ds2+~3.11.2+ds1/cctbx.egg-info/top_level.txt
>  cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx.egg-info/PKG-INFO
>  cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx.egg-info/SOURCES.txt
>  cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx.egg-info/dependency_links.txt
>  cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx.egg-info/entry_points.txt
>  cctbx-2022.9+ds2+~3.11.2+ds1/dxtbx/src/dxtbx.egg-info/top_level.txt
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/cctbx_2022.9+ds2+~3.11.2+ds1-6.diff.FyrFA2
> 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/cctbx_2022.9+ds2+~3.11.2+ds1-6_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.