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

Julian Gutekunst j.gutekunst at dkfz-heidelberg.de
Tue Jul 29 16:27:57 BST 2014

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 
panic: sv_setpvn called with negative strlen -1 at 
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?

Julian Gutekunst

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