[Debichem-devel] Bug#1009383: gromacs: FTBFS: AttributeError: module 'collections' has no attribute 'Iterable'

[Lucas Nussbaum]

Source: gromacs
Version: 2021.4-2
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220412 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> make[4]: Entering directory '/<<PKGBUILDDIR>>/build/documentation'
> cd /<<PKGBUILDDIR>>/build/documentation/docs/doxygen && /usr/bin/python3.10 /<<PKGBUILDDIR>>/docs/doxygen/graphbuilder.py -S /<<PKGBUILDDIR>> -B /<<PKGBUILDDIR>>/build/documentation --ignore-cycles /<<PKGBUILDDIR>>/docs/doxygen/cycle-suppressions.txt -o /<<PKGBUILDDIR>>/build/documentation/docs/doxygen/depgraphs
> cd /<<PKGBUILDDIR>>/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake
> NOTE: You are using Doxygen version 1.9.1. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings.
> Running Doxygen...
> warning: Tag 'MSCGEN_PATH' at line 36 of file 'Doxyfile-common' has become obsolete.
>          To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
> Scanning source tree...
> Reading source files...
> Reading Doxygen XML files...
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/docs/doxygen/graphbuilder.py", line 562, in <module>
>     main()
>   File "/<<PKGBUILDDIR>>/docs/doxygen/graphbuilder.py", line 538, in main
>     tree.load_xml(only_files=True)
>   File "/<<PKGBUILDDIR>>/docs/doxygen/gmxtree.py", line 819, in load_xml
>     if isinstance(only_files, collections.Iterable):
> AttributeError: module 'collections' has no attribute 'Iterable'
> make[4]: *** [docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make:76: docs/doxygen/dep-graphs-dot-timestamp.txt] Error 1


The full build log is available from:
http://qa-logs.debian.net/2022/04/12/gromacs_2021.4-2_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220412;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220412&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 marking 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.