Your message dated Sun, 08 Dec 2024 23:29:32 +0000
with message-id <e1tkqis-00fkfz...@fasolo.debian.org>
and subject line Bug#1048635: fixed in unicycler 0.5.1+dfsg-1.1
has caused the Debian Bug report #1048635,
regarding unicycler: Fails to build source after successful build
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1048635: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1048635
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: unicycler
Version: 0.5.0+dfsg-1
Severity: minor
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-sab-20230813 ftbfs-source-after-build
User: debian...@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 unicycler
> dpkg-buildpackage: info: source version 0.5.0+dfsg-1
> dpkg-buildpackage: info: source distribution unstable
> dpkg-buildpackage: info: source changed by Andreas Tille <ti...@debian.org>
> dpkg-source --before-build .
> debian/rules clean
> dh clean --with python3 --buildsystem=pybuild
> debian/rules override_dh_auto_clean
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> find . -name __pycache__ -type d | xargs rm -rf
> make distclean
> make[2]: Entering directory '/<<PKGBUILDDIR>>'
> Platform: Linux
> Compiler: g++ 13.2.0
> rm -f unicycler/src/scoredalignment.o unicycler/src/minimap_align.o
> unicycler/src/ref_seqs.o unicycler/src/random_alignments.o
> unicycler/src/miniasm/asm.o unicycler/src/miniasm/sdict.o
> unicycler/src/miniasm/dotter.o unicycler/src/miniasm/asg.o
> unicycler/src/miniasm/sys.o unicycler/src/miniasm/paf.o
> unicycler/src/miniasm/hit.o unicycler/src/consensus_align.o
> unicycler/src/global_align.o unicycler/src/semi_global_align.o
> unicycler/src/string_functions.o unicycler/src/miniasm_assembly.o
> unicycler/src/start_end_align.o unicycler/src/path_align.o
> unicycler/src/minimap/misc.o unicycler/src/minimap/map.o
> unicycler/src/minimap/sdust.o unicycler/src/minimap/bseq.o
> unicycler/src/minimap/sketch.o unicycler/src/minimap/kthread.o
> unicycler/src/minimap/index.o unicycler/src/semi_global_align_exhaustive.o
> unicycler/src/overlap_align.o unicycler/src/kmers.o
> rm -f unicycler/cpp_functions.so
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_autoreconf_clean -O--buildsystem=pybuild
> dh_clean -O--buildsystem=pybuild
> dpkg-source -b .
> dpkg-source: info: using source format '3.0 (quilt)'
> dpkg-source: info: building unicycler using existing
> ./unicycler_0.5.0+dfsg.orig.tar.xz
> dpkg-source: info: using patch list from debian/patches/series
> dpkg-source: warning: newly created empty file
> '.pybuild/cpython3_3.11_unicycler/build/unicycler/__init__.py' will not be
> represented in diff
> dpkg-source: error: cannot represent change to
> .pybuild/cpython3_3.11_unicycler/build/unicycler/cpp_functions.so: binary
> file contents changed
> dpkg-source: error: add
> .pybuild/cpython3_3.11_unicycler/build/unicycler/cpp_functions.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_unicycler/build/unicycler/cpp_functions.so' will not
> be represented in diff
> dpkg-source: warning: file
> unicycler-0.5.0+dfsg/unicycler.egg-info/SOURCES.txt has no final newline
> (either original or modified version)
> 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/unicycler_0.5.0+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.
--- End Message ---
--- Begin Message ---
Source: unicycler
Source-Version: 0.5.1+dfsg-1.1
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
unicycler, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1048...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated unicycler package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 08 Dec 2024 22:50:24 +0100
Source: unicycler
Architecture: source
Version: 0.5.1+dfsg-1.1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1048635 1087157
Changes:
unicycler (0.5.1+dfsg-1.1) unstable; urgency=medium
.
* Team upload.
.
[ Michael R. Crusoe ]
* salsa ci: skip i386
.
[ Étienne Mollier ]
* spades.patch: unfuzz hunk with offset.
* d/clean: new: remove leftover .pybuild and egg info. (Closes: #1048635)
* leftover-syntax-warnings.patch: fix remaining SyntaxWarnings.
(Closes: #1087157)
* d/patches/*: normalize last-update timestamp.
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