Your message dated Sat, 20 Apr 2024 09:05:33 +0000
with message-id <e1ry6f7-00axlt...@fasolo.debian.org>
and subject line Bug#1066369: fixed in obitools 1.2.13+dfsg-8
has caused the Debian Bug report #1066369,
regarding obitools: FTBFS:
build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:6320:3:
error: implicit declaration of function ‘heapsort’
[-Werror=implicit-function-declaration]
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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--
1066369: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066369
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: obitools
Version: 1.2.13+dfsg-7
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240313 ftbfs-trixie ftbfs-impfuncdef
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
This is most likely caused by a change in dpkg 1.22.6, that enabled
-Werror=implicit-function-declaration. For more information, see
https://wiki.debian.org/qa.debian.org/FTBFS#A2024-03-13_-Werror.3Dimplicit-function-declaration
Relevant part (hopefully):
> x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -g -O2
> -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -fstack-clash-protection -Wformat
> -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
> -Isrc/obitools/word -I/usr/include/python3.11 -c
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c -o
> build/temp.linux-x86_64-cpython-311/build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.o
> -msse2
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c: In
> function ‘__pyx_pf_8obitools_4word_10_readindex_9ReadIndex_10indexWords’:
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:6320:3:
> error: implicit declaration of function ‘heapsort’
> [-Werror=implicit-function-declaration]
> 6320 | heapsort(__pyx_v_self->_wordlist, __pyx_v_i, (sizeof(pobinuc)),
> __pyx_f_8obitools_4word_10_readindex_cmpwords);
> | ^~~~~~~~
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c: In
> function ‘__pyx_gb_8obitools_4word_10_readindex_9ReadIndex_14generator’:
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:6589:33:
> warning: comparison of integer expressions of different signedness: ‘size_t’
> {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 6589 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
> | ^
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c: In
> function ‘__pyx_gb_8obitools_4word_10_readindex_9ReadIndex_17generator1’:
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:6787:33:
> warning: comparison of integer expressions of different signedness: ‘size_t’
> {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 6787 | for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
> | ^
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c: In
> function ‘__pyx_pf_8obitools_4word_10_readindex_9ReadIndex_8load’:
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:5495:10:
> warning: ignoring return value of ‘fread’ declared with attribute
> ‘warn_unused_result’ [-Wunused-result]
> 5495 | (void)(fread((&__pyx_v_ltbuffer), (sizeof(size_t)), 1, __pyx_v_f));
> | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:5564:10:
> warning: ignoring return value of ‘fread’ declared with attribute
> ‘warn_unused_result’ [-Wunused-result]
> 5564 | (void)(fread(__pyx_v_tcbuffer, 1, __pyx_v_ltbuffer, __pyx_v_f));
> | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:5749:10:
> warning: pointer ‘__pyx_v_f’ may be used after ‘fclose’ [-Wuse-after-free]
> 5749 | (void)(fclose(__pyx_v_f));
> | ~^~~~~~~~~~~~~~~~~~
> build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:5616:10:
> note: call to ‘fclose’ here
> 5616 | (void)(fclose(__pyx_v_f));
> | ~^~~~~~~~~~~~~~~~~~
> cc1: some warnings being treated as errors
> error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1
> E: pybuild pybuild:389: build: plugin distutils failed with: exit code=1:
> /usr/bin/python3 setup.py build
> dh_auto_build: error: pybuild --build -i python{version} -p 3.11 returned
> exit code 13
> make: *** [debian/rules:15: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2024/03/13/obitools_1.2.13+dfsg-7_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240313;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
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: obitools
Source-Version: 1.2.13+dfsg-8
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
obitools, 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 1066...@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 obitools 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: Sat, 20 Apr 2024 10:41:15 +0200
Source: obitools
Architecture: source
Version: 1.2.13+dfsg-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1066369
Changes:
obitools (1.2.13+dfsg-8) unstable; urgency=medium
.
* Team upload.
* qsort.patch: new: replace heapsort by qsort. (Closes: #1066369)
* d/control: declare compliance to standards version 4.7.0.
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