[ensembl-dev] panic: sv_setpvn error on local setup

Dan Sheppard dan at ebi.ac.uk
Wed Jul 30 11:55:11 BST 2014

Hi Julian,

It's hard to be definitive as I've not been able to reproduce thee 
issue. I suspect it's some complex interaction of perl version, libc, 
bit-width, etc, and we don't have a machine exactly matching your spec 
readily available. The other possibility is that this error is masking 
some deeper misconfiguration.

But, assuming that the bad sv_setpvn is from the caller() on the line 
indicated in the error (and the perl RT suggests there's a history of 
such dodgy practices in caller()), I think the best thing to do is to 
effectively comment out that block of code, by changing the if(1) to 
if(0) on line 122.

I've not had a chance to do the archaeology yet, but it looks like that 
code is only there for debugging purposes. I've checked that this 
doesn't immediately break the site via my sandbox, but caveat emptor. 
Let us know how you get on and we can proceed from there.

Thanks for providing a detailed report, that helps enormously.


On 29/07/14 16:27, Julian Gutekunst wrote:
> Hello everybody,
> I am trying to set up a local version of the Ensembl Website including a
> local database structure with the intention of running the automated
> annotation pipeline (Genebuild) and providing the Genome via the Ensembl
> genome browser. So far, I followed the tutorial provided by the Ensembl
> website and everything went more or less fine.
> I have everything installed (every required module/library, apache,
> perl, the website code, database structure, and even downloaded a genome
> from the Ensembl database for testing).
> Now, the problem I currently facing is when starting the Apache server
> using the command:
> /usr/local/apache2.2.27/bin/httpd -d /usr/local/ensembl/ensembl-webcode/
> The Apache server tries to load all provided databases but crashes (at
> random timepoints while loading) with the following error message:
> Syntax error on line 152 of
> /usr/local/ensembl/ensembl-webcode/conf/httpd.conf:
> panic: sv_setpvn called with negative strlen -1 at
> /usr/local/ensembl/ensembl-webcode/modules/EnsEMBL/Web/SpeciesDefs.pm
> line 125.\n
> This error was only once posted here, but there was never a definite
> answer for fixing this problem. Since I've read somewhere that this
> might be a Perl-related bug I also tested to run the website with
> different versions of Perl (using perlbrew) but the error still appears.
> Further details on my setup:
> OS: openSUSE 13.1 (x86_64)
> Perl 5.18.1
> Apache 2.2.27
> mod_perl 2.8
> mysql 5.5.33-MariaDB openSUSE package
> What can I try to fix this problem?
> Sincerely,
> Julian Gutekunst

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