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AGAT compatible with Perl 5.36 ? #392

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eylenth opened this issue Aug 23, 2023 · 10 comments
Closed

AGAT compatible with Perl 5.36 ? #392

eylenth opened this issue Aug 23, 2023 · 10 comments
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@eylenth
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eylenth commented Aug 23, 2023

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):

  • AGAT version 1.2.0/1.1.0
  • AGAT installation: Manual/EasyBuild
  • OS: RedHat 7.9

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
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Juke34 commented Jan 12, 2024

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
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eylenth commented Feb 12, 2024

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 Juke34 reopened this Feb 13, 2024
@Juke34
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Juke34 commented Feb 14, 2024

Maybe same problem as here: #424 (comment)

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
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eylenth commented Feb 14, 2024

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

@EXGDT
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EXGDT commented Mar 7, 2024

@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
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Juke34 commented Mar 7, 2024

Interesting, thank you for the feedbacks

@Juke34 Juke34 added the help wanted Extra attention is needed label Apr 4, 2024
@boegel
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boegel commented Sep 24, 2024

Are there any updates on figuring this out?

We're still getting reports with the problem with AGAT 1.4.0...

@Juke34
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Juke34 commented Sep 24, 2024

No update sorry

Juke34 added a commit that referenced this issue Dec 3, 2024
…AGAT::Module->export_to_level(1,@_) from AGAT::AGAT. This fix issiue related to replace export_to_level(2,@_) introduced in perl 5.36. Fix #416 #392
Juke34 added a commit that referenced this issue Dec 3, 2024
* add dockerfile for AGAT with perl version 536

* replace export_to_level(2,@_) in each module called by AGAT::AGAT by AGAT::Module->export_to_level(1,@_) from AGAT::AGAT. This fix issiue related to replace export_to_level(2,@_) introduced in perl 5.36. Fix #416 #392

* add test for perl>5.36

* remove indentation in shebang

* add missing semicolon

* run make test for first job
@Juke34
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Juke34 commented Dec 3, 2024

Now fixed in master branch via PR #509 #509

@Juke34 Juke34 closed this as completed Dec 3, 2024
@eylenth
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eylenth commented Dec 5, 2024

hi @Juke34
Thanks for the patch.
It works fine now.

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