Source: obitools
Version: 1.2.13+dfsg-7
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas@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=lucas@debian.org
or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240313&fusertaguser=lucas@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.

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Hi,

Lucas Nussbaum, on 2024-03-13:

build/temp.linux-x86_64-cpython-311/pyrex/obitools/word/_readindex.c:6320:3: error: implicit declaration of function ‘heapsort’ [-Werror=implicit-function-declaration]

Interesting, if I trust the Debian online manual of heapsort[1],
this is a Berkeley function optimized for "almost" sorted
arrays. I see two options here: either try to implement the
libbsd compatibility layer in cython context, or replace
heapsort by qsort[2] (and remove the heapsort function
declaration from the .pyx); the two functions look to have
compatible argument passing.

I would consider implementing the replacement by qsort: this may
affect the memory consumption, and possibly performances of
obitools; on the other hand I wonder how come the program
managed to do the sorting without appropriate function available
in the application binary interface in the first place.

[1]: https://manpages.debian.org/bookworm/libbsd-dev/heapsort.3bsd.en.html
[2]: https://manpages.debian.org/bookworm/manpages-fr-dev/qsort.3.fr.html

Have a nice day, :)
--
.''`. Étienne Mollier <emollier@debian.org>
: :' : pgp: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da
`. `' sent from /dev/pts/1, please excuse my verbosity
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Processing control commands:

tag -1 pending

Bug #1066369 [src:obitools] 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]
Added tag(s) pending.

--
1066369: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1066369
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

Control: tag -1 pending

Hello,

Bug #1066369 in obitools reported by you has been fixed in the
Git repository and is awaiting an upload. You can see the commit
message below and you can check the diff of the fix at:

https://salsa.debian.org/med-team/obitools/-/commit/fb6053e4a8742128194a416438fa695959b2e0ff

------------------------------------------------------------------------ qsort.patch: new: replace heapsort by qsort.

Closes: #1066369 ------------------------------------------------------------------------

(this message was generated automatically)
--
Greetings

https://bugs.debian.org/1066369

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

This is a multi-part message in MIME format...

Your message dated Sat, 20 Apr 2024 09:05:33 +0000
with message-id <E1ry6f7-00AxLT-U7@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 owner@bugs.debian.org with problems

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