[R-pkg-team] Bug#1045706: r-bioc-rhdf5filters: Fails to build source after successful build

[Lucas Nussbaum]

Source: r-bioc-rhdf5filters
Version: 1.12.1+dfsg-2
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 r-bioc-rhdf5filters
> dpkg-buildpackage: info: source version 1.12.1+dfsg-2
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh at debian.org>
>  dpkg-source --before-build .
>  debian/rules clean
> dh clean --buildsystem R
>    dh_auto_clean -O--buildsystem=R
>    dh_autoreconf_clean -O--buildsystem=R
> 	rm -f -- ./autom4te.cache/requests ./autom4te.cache/traces.2 ./autom4te.cache/output.2 ./autom4te.cache/output.1 ./autom4te.cache/traces.1 ./autom4te.cache/output.0 ./autom4te.cache/traces.0 ./configure
> 	rm -f debian/autoreconf.before debian/autoreconf.after
>    dh_clean -O--buildsystem=R
> 	rm -f debian/debhelper-build-stamp
> 	rm -rf debian/.debhelper/
> 	rm -f -- debian/r-bioc-rhdf5filters.substvars debian/files
> 	rm -fr -- debian/r-bioc-rhdf5filters/ debian/tmp/
> 	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 r-bioc-rhdf5filters using existing ./r-bioc-rhdf5filters_1.12.1+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: executable mode 0755 of 'config.status' will not be represented in diff
> dpkg-source: error: cannot represent change to src/blosc/H5Zblosc.o: binary file contents changed
> dpkg-source: error: add src/blosc/H5Zblosc.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 src/blosc/libH5Zblosc.so: binary file contents changed
> dpkg-source: error: add src/blosc/libH5Zblosc.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 'src/blosc/libH5Zblosc.so' will not be represented in diff
> dpkg-source: error: cannot represent change to src/bzip2/libH5Zbz2.so: binary file contents changed
> dpkg-source: error: add src/bzip2/libH5Zbz2.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 'src/bzip2/libH5Zbz2.so' will not be represented in diff
> dpkg-source: error: cannot represent change to src/lzf/libH5Zlzf.so: binary file contents changed
> dpkg-source: error: add src/lzf/libH5Zlzf.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 'src/lzf/libH5Zlzf.so' will not be represented in diff
> dpkg-source: error: cannot represent change to src/lzf/lzf/liblzf.a: binary file contents changed
> dpkg-source: error: add src/lzf/lzf/liblzf.a in debian/source/include-binaries if you want to store the modified binary in the debian tarball
> dpkg-source: error: cannot represent change to src/lzf/lzf/lzf_c.o: binary file contents changed
> dpkg-source: error: add src/lzf/lzf/lzf_c.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 src/lzf/lzf/lzf_d.o: binary file contents changed
> dpkg-source: error: add src/lzf/lzf/lzf_d.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/r-bioc-rhdf5filters_1.12.1+dfsg-2_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.