[Debian-med-packaging] Bug#1047612: macs: Fails to build source after successful build

[Lucas Nussbaum]

Source: macs
Version: 2.2.9.1-1
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 macs
> dpkg-buildpackage: info: source version 2.2.9.1-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe at debian.org>
>  dpkg-source --before-build .
> dpkg-source: info: using options from macs-2.2.9.1/debian/source/options: --extend-diff-ignore=(^|/)(.*\.c)$|.*[.]egg-info/
>  debian/rules clean
> dh clean --buildsystem=pybuild
>    debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> rm -Rf test/macs2.2.9.1-1* test/speedtest*
> rm -f debian/*.1 debian/*-man-include
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_autoreconf_clean -O--buildsystem=pybuild
>    dh_clean -O--buildsystem=pybuild
>  dpkg-source -b .
> dpkg-source: info: using options from macs-2.2.9.1/debian/source/options: --extend-diff-ignore=(^|/)(.*\.c)$|.*[.]egg-info/
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building macs using existing ./macs_2.2.9.1.orig.tar.gz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/BedGraph.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/BedGraph.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/BedGraph.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/BedGraphIO.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/BedGraphIO.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/BedGraphIO.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/CallPeakUnit.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/CallPeakUnit.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/CallPeakUnit.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/FixWidthTrack.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/FixWidthTrack.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/FixWidthTrack.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/PairedEndTrack.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/PairedEndTrack.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/PairedEndTrack.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/Parser.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/Parser.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/Parser.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/PeakIO.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/PeakIO.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/PeakIO.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/ScoreTrack.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/ScoreTrack.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/ScoreTrack.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: warning: newly created empty file '.pybuild/cpython3_3.11_MACS2/build/MACS2/IO/__init__.py' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/__pycache__/__init__.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/IO/__pycache__/__init__.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/PeakDetect.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/PeakDetect.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/PeakDetect.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/PeakModel.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/PeakModel.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/PeakModel.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/Pileup.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/Pileup.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/Pileup.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/Prob.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/Prob.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/Prob.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/Signal.cpython-311-x86_64-linux-gnu.so: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/Signal.cpython-311-x86_64-linux-gnu.so in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of '.pybuild/cpython3_3.11_MACS2/build/MACS2/Signal.cpython-311-x86_64-linux-gnu.so' will not be represented in diff
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/Constants.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/Constants.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/OptValidator.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/OptValidator.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/OutputWriter.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/OutputWriter.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/__init__.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/__init__.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgbroadcall_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgbroadcall_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgcmp_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgcmp_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgdiff_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgdiff_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgopt_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgopt_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgpeakcall_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/bdgpeakcall_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/callpeak_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/callpeak_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/cmbreps_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/cmbreps_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/filterdup_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/filterdup_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/pileup_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/pileup_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/predictd_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/predictd_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/randsample_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/randsample_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/refinepeak_cmd.cpython-311.pyc: binary file contents changed
> dpkg-source: error: add .pybuild/cpython3_3.11_MACS2/build/MACS2/__pycache__/refinepeak_cmd.cpython-311.pyc in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: warning: executable mode 0755 of 'build/scripts-3.11/macs2' will not be represented in diff
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/IO/BedGraph.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/IO/BedGraph.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/IO/BedGraphIO.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/IO/BedGraphIO.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/IO/CallPeakUnit.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/IO/CallPeakUnit.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/IO/FixWidthTrack.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/IO/FixWidthTrack.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/IO/PairedEndTrack.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/IO/PairedEndTrack.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/IO/Parser.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/IO/Parser.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/IO/PeakIO.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/IO/PeakIO.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/IO/ScoreTrack.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/IO/ScoreTrack.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/PeakDetect.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/PeakDetect.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/PeakModel.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/PeakModel.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/Pileup.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/Pileup.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/Prob.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/Prob.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/Signal.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/Signal.o in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to build/temp.linux-x86_64-cpython-311/MACS2/cPosValCalculation.o: binary file contents changed
> dpkg-source: error: add build/temp.linux-x86_64-cpython-311/MACS2/cPosValCalculation.o 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/macs_2.2.9.1-1_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.