[Debian-med-packaging] Bug#1043666: biosig: Fails to build source after successful build

Lucas Nussbaum lucas at debian.org
Sun Aug 13 14:17:55 BST 2023 

Source: biosig
Version: 2.5.0-1
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 biosig
> dpkg-buildpackage: info: source version 2.5.0-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh  clean --with python3,numpy3,octave
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> if [ -f biosig4c++/python//setup.py ] ; then pybuild --clean ; fi
> I: pybuild base:275: python3.11 setup.py clean 
> /<<PKGBUILDDIR>>/biosig4c++/python/setup.py:35: DeprecationWarning: 
> 
>   `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
>   of the deprecation of `distutils` itself. It will be removed for
>   Python >= 3.12. For older Python versions it will remain present.
>   It is recommended to use `setuptools < 60.0` for those Python versions.
>   For more details, see:
>     https://numpy.org/devdocs/reference/distutils_status_migration.html 
> 
> 
>   import numpy.distutils.misc_util
> running clean
> removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_biosig/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
> dh_auto_clean
> 	make -j8 distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> make -C biosig4c++/mma clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/mma'
> ls: cannot access '/SystemFiles/Links/MathLink/DeveloperKit/*': No such file or directory
> mliver.c:5:10: fatal error: mathlink.h: No such file or directory
>     5 | #include <mathlink.h>
>       |          ^~~~~~~~~~~~
> compilation terminated.
> rm -f *.o* */*.o*
> rm -f *tm.c */*tm.c
> rm -f *.exe */*.exe
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/mma'
> make -C biosig4c++ clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++'
> rm -f *~
> rm -f *.a
> rm -f *.def
> rm -f *.dll
> rm -f *.dll.a
> rm -f *.i
> rm -f *.o
> rm -f *.so *.dylib
> rm -f *.so.*
> rm -f *.oct
> rm -f libbiosig.pc
> rm -f test/t1.*
> rm -f win32/*.exe win32/*.o* win32/*.lib win32/*.a
> rm -f win64/*.exe win64/*.o* win64/*.lib win64/*.a
> rm -f t240/*.o*
> rm -f t240/libcnsfef.a
> rm -f libbiosig.* libbiosig3.*
> rm -f pdp2gdf save2gdf physicalunits biosig_fhir biosig2gdf
> rm -f mma/biosig.exe mma/*/biosig.exe
> make -C java clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/java'
> rm *.h
> rm: cannot remove '*.h': No such file or directory
> make[4]: [Makefile:33: clean] Error 1 (ignored)
> rm *.o 
> rm: cannot remove '*.o': No such file or directory
> make[4]: [Makefile:34: clean] Error 1 (ignored)
> rm *.cxx 
> rm: cannot remove '*.cxx': No such file or directory
> make[4]: [Makefile:35: clean] Error 1 (ignored)
> rm *.so
> rm: cannot remove '*.so': No such file or directory
> make[4]: [Makefile:36: clean] Error 1 (ignored)
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/java'
> make -C mex clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/mex'
> rm -f *.o *.obj *.o64 core octave-core *.oct *.mex* mexSOPEN.cpp
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/mex'
> rm -f mex/mexbiosig*.src.tar.gz
> rm -f mex/biosig4octave*.src.tar.gz
> make -C mma clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/mma'
> ls: cannot access '/SystemFiles/Links/MathLink/DeveloperKit/*': No such file or directory
> mliver.c:5:10: fatal error: mathlink.h: No such file or directory
>     5 | #include <mathlink.h>
>       |          ^~~~~~~~~~~~
> compilation terminated.
> rm -f *.o* */*.o*
> rm -f *tm.c */*tm.c
> rm -f *.exe */*.exe
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/mma'
> make -C php clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/php'
> rm *.h 
> rm: cannot remove '*.h': No such file or directory
> make[4]: [Makefile:19: clean] Error 1 (ignored)
> rm *.o 
> rm: cannot remove '*.o': No such file or directory
> make[4]: [Makefile:20: clean] Error 1 (ignored)
> rm *.cpp 
> rm: cannot remove '*.cpp': No such file or directory
> make[4]: [Makefile:21: clean] Error 1 (ignored)
> rm *.so
> rm: cannot remove '*.so': No such file or directory
> make[4]: [Makefile:22: clean] Error 1 (ignored)
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/php'
> make -C perl clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/perl'
> rm *.cxx 
> rm: cannot remove '*.cxx': No such file or directory
> make[4]: [Makefile:21: clean] Error 1 (ignored)
> rm *.o
> rm: cannot remove '*.o': No such file or directory
> make[4]: [Makefile:22: clean] Error 1 (ignored)
> rm *.pm
> rm: cannot remove '*.pm': No such file or directory
> make[4]: [Makefile:23: clean] Error 1 (ignored)
> rm *.so
> rm: cannot remove '*.so': No such file or directory
> make[4]: [Makefile:24: clean] Error 1 (ignored)
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/perl'
> make -C R clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/R'
> rm *.o *.so *.gz biosig_2.5.0.tar.gz
> rm: cannot remove '*.o': No such file or directory
> rm: cannot remove '*.so': No such file or directory
> rm: cannot remove '*.gz': No such file or directory
> rm: cannot remove 'biosig_2.5.0.tar.gz': No such file or directory
> make[4]: *** [Makefile:10: clean] Error 1
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/R'
> make[3]: [Makefile:977: clean] Error 2 (ignored)
> make -C ruby clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/ruby'
> rm *.cxx
> rm: cannot remove '*.cxx': No such file or directory
> make[4]: [Makefile:20: clean] Error 1 (ignored)
> rm *.o
> rm: cannot remove '*.o': No such file or directory
> make[4]: [Makefile:21: clean] Error 1 (ignored)
> rm *.pm
> rm: cannot remove '*.pm': No such file or directory
> make[4]: [Makefile:22: clean] Error 1 (ignored)
> rm *.so
> rm: cannot remove '*.so': No such file or directory
> make[4]: [Makefile:23: clean] Error 1 (ignored)
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/ruby'
> make -C tcl clean
> make[4]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/tcl'
> rm *.cxx
> rm: cannot remove '*.cxx': No such file or directory
> make[4]: [Makefile:19: clean] Error 1 (ignored)
> rm *.o 
> rm: cannot remove '*.o': No such file or directory
> make[4]: [Makefile:20: clean] Error 1 (ignored)
> rm *.so
> rm: cannot remove '*.so': No such file or directory
> make[4]: [Makefile:21: clean] Error 1 (ignored)
> make[4]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/tcl'
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++'
> rm mexbiosig*.src.tar.gz
> rm: cannot remove 'mexbiosig*.src.tar.gz': No such file or directory
> make[2]: [Makefile:44: clean] Error 1 (ignored)
> rm biosig4octave*.src.tar.gz
> make -C biosig4c++/python clean
> make[3]: Entering directory '/<<PKGBUILDDIR>>/biosig4c++/python'
> rm -rf build/*
> rm -rf dist/*
> rm *.so
> rm: cannot remove '*.so': No such file or directory
> make[3]: [Makefile:32: clean] Error 1 (ignored)
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/biosig4c++/python'
> rm config.log
> rm config.status
> rm Makefile biosig4c++/Makefile biosig4c++/*/Makefile \
> 	biosig4c++/python/setup.py \
> 	biosig4c++/R/DESCRIPTION
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean
>    dh_clean
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building biosig using existing ./biosig_2.5.0.orig.tar.xz
> dpkg-source: warning: ignoring deletion of file config.log, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file install-sh, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file configure, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file config.h.in, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file config.status, use --include-removal to override
> dpkg-source: warning: ignoring deletion of directory autom4te.cache
> dpkg-source: warning: ignoring deletion of file autom4te.cache/requests, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autom4te.cache/output.1, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autom4te.cache/traces.1, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autom4te.cache/output.0, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file autom4te.cache/traces.0, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/units.i, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/11073-10102-AnnexB.i, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/eventcodes.i, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/eventcodegroups.i, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/t240/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/magic/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/tcl/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/igor/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/examples/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/php/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/mma/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/perl/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/mex/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/t241/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/R/DESCRIPTION, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/R/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/java/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/ruby/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/python/Makefile, use --include-removal to override
> dpkg-source: warning: ignoring deletion of file biosig4c++/python/setup.py, use --include-removal to override
> dpkg-source: info: local changes detected, the modified files are:
>  biosig-2.5.0/config.h
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/biosig_2.5.0-1.diff.TU0m6g
> 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/biosig_2.5.0-1_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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