[Debian-med-packaging] Bug#1045139: eigensoft: Fails to build source after successful build

[Lucas Nussbaum]

Source: eigensoft
Version: 8.0.0+dfsg-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 eigensoft
> dpkg-buildpackage: info: source version 8.0.0+dfsg-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
>    debian/rules override_dh_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_clean
> /usr/bin/make -C src clobber
> make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
> rm -f *.o */*.o */*.a nicksrc/*.o eigensrc/*.o ksrc/*.o
> rm -f baseprog convertf mergeit pca eigensrc/pcatoy eigensrc/smartrel eigensrc/smarteigenstrat eigensrc/twstats eigensrc/eigenstrat eigensrc/eigenstratQTL eigensrc/smartpca
> cd ../bin/ ; rm -f baseprog convertf mergeit pca pcatoy smartrel smarteigenstrat twstats eigenstrat eigenstratQTL smartpca ; cd ../src
> make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>  dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building eigensoft using existing ./eigensoft_8.0.0+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: info: local changes detected, the modified files are:
>  eigensoft-8.0.0+dfsg/POPGEN/elldemo/doplot
>  eigensoft-8.0.0+dfsg/POPGEN/elldemo/rescale_ell
>  eigensoft-8.0.0+dfsg/bin/ploteig
>  eigensoft-8.0.0+dfsg/bin/rescale_ell
> dpkg-source: error: aborting due to unexpected upstream changes, see /tmp/eigensoft_8.0.0+dfsg-1.diff.uuFvVK
> 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/eigensoft_8.0.0+dfsg-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.