Bug 587608

Summary:	dev-perl/forks-0.360.0 - fix incompatibility with >=perl-5.18
Product:	Gentoo Linux	Reporter:	Martin Mokrejš <mmokrejs>
Component:	Current packages	Assignee:	Gentoo Perl team <perl>
Status:	RESOLVED FIXED
Severity:	normal
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

Description Martin Mokrejš 2016-06-30 19:04:28 UTC

I think I hit this bug already but did not report it. It came now through a maker-devel email list and provided 0.360.0 version was released 27 Jun 2014 it should be still relevant issue for my current perl-5.20.1 install.

From Carson Holt
Subject: Re: [maker-devel] Segmentation Fault
Date: Thu, 30 Jun 2016 12:11:31 -0600

...

Finally the error from the forks module. See the following from the devel list —> https://groups.google.com/forum/#!topic/maker-devel/2kYQ90TCuXA
It can be fixed with a small edit to the forks.pm file from CPAN (or a change in perl version)

—Carson

> On Jun 28, 2016, at 7:24 PM, Madolyn Macdonald <mmacd@udel.edu> wrote:
>
> Hi Maker,
> I am trying to run Maker and got the following in my stderr.log file for one of my scaffolds.
>
> sh: line 1: 34865 Segmentation fault      (core dumped) /usr/local/exonerate-2.2.0/bin/exonerate -q /tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t /tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm line 1736.
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm line 1736.
> ERROR: Exonerate failed
> --> rank=1, hostname=biomix2.dbi.local
> ERROR: Failed while polishing proteins
> ERROR: Chunk failed at level:10, tier_type:3
> FAILED CONTIG:picr50
>
...
> _______________________________________________
> maker-devel mailing list
> maker-devel@box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

BTW, I do not see it even reported in https://rt.cpan.org/Public/Dist/Display.html?Name=forks . Anybody haviong time to report there?  ;) Thank you.

Comment 1 Andreas K. Hüttel archtester

2016-12-29 16:44:27 UTC

Tests of forks pass here (with 5.24.1-rc4); is this still a problem?

Comment 2 Martin Mokrejš 2017-01-06 19:43:29 UTC

Do not know, I was hoping somebody checks the old patch content and whatever is the current version. ;)

Comment 3 Andreas K. Hüttel archtester

2017-03-12 23:16:38 UTC

(In reply to Martin Mokrejš from comment #2)
> Do not know, I was hoping somebody checks the old patch content and whatever
> is the current version. ;)

OK let's assume it is fixed...