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NBISweden / AGAT

Another Gtf/Gff Analysis Toolkit
GNU General Public License v3.0
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AGAT compatible with Perl 5.36 ? #392

Open eylenth opened 10 months ago

eylenth commented 10 months ago

Describe the bug We are trying to run AGAT which is built with Perl 5.36 and more recent Perl packages, but we are getting Undefined subroutine error messages. We did the same tests with AGAT(same version), which is built with Perl 5.32, where we are getting the expected output.

General (please complete the following information):

To Reproduce

 $ agat_convert_sp_gxf2gxf.pl --gff 8_test.gff
Using standard /tools/eb/software/AGAT/1.1.0-GCC-12.2.0/lib/perl5/site_perl/5.36.0/auto/share/dist/AGAT/config.yaml file
Undefined subroutine &main::prepare_gffout called at /tools/eb/software/AGAT/1.1.0-GCC-12.2.0/bin/agat_convert_sp_gxf2gxf.pl line 47.
 $ agat_sp_statistics.pl --gff 8_test.gff -o stats.txt
Using standard /tools/eb/software/AGAT/1.1.0-GCC-12.2.0/lib/perl5/site_perl/5.36.0/auto/share/dist/AGAT/config.yaml file
Undefined subroutine &main::prepare_fileout called at /tools/eb/software/AGAT/1.1.0-GCC-12.2.0/bin/agat_sp_statistics.pl line 50.

Expected behavior A lot of output related that the job is finished.

Additional context EasyBuild is used to build AGAT from source: https://github.com/easybuilders/easybuild-easyconfigs/blob/develop/easybuild/easyconfigs/a/AGAT/AGAT-1.1.0-GCC-12.2.0.eb

Juke34 commented 5 months ago

It should be compatible with 5.36 yes. I think it is just because no output file that was provided. (If I remember well in version 1.1.0 providing an output was mandatory ). It has been fixed in next release.

eylenth commented 4 months ago

hi @Juke34

It seems that this issue is still not solved with the latest release. I have built AGAT with the latest commit: bea962b

Juke34 commented 4 months ago

Maybe same problem as here: https://github.com/NBISweden/AGAT/issues/424#issuecomment-1942917802

I have to figure out how easy build works. You mean just changing the perl version from 5.32 to 5.36 make it breaks?

eylenth commented 4 months ago

@Juke34 Yes indeed. Working fine with Perl 5.32 Not working anymore with Perl 5.36

EXGDT commented 4 months ago

@Juke34 Yes indeed. Working fine with Perl 5.32 Not working anymore with Perl 5.36

I encountered the same issue with Perl 5.38. It was resolved after I downgraded from Perl 5.38 to 5.32.

Juke34 commented 4 months ago

Interesting, thank you for the feedbacks