[Debian-med-packaging] Bug#1066369: 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]

[Lucas Nussbaum]

Source: obitools
Version: 1.2.13+dfsg-7
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at 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.