Good to hear that it worked for you... cheers syed
> Hi Syed, > > The cause of the problem I was having seems to have been perl. Since > mod_perl was compiling and passing all its tests, I figured that the > problem must be with the perl modules conflicting in some way. So, I > built an entirely separate and clean version of perl. I then loaded > only the modules that Biomart needs, and then rebuilt mod_perl. It took > a little more tweaking of the libraries for mod_perl before I finally > got the martview to work. > > Thanks for you help diagnosing the problem. > > Mike > > Syed Haider wrote: >> Hi Mike, >> the investigation and error suggests there is something wrong with your >> mod_perl integration. you call any of martview or martservice scripts, >> it stays the same. You need to check it somehow. I have not seen exactly >> the same problem before but I would reinstall the apache with mod_perl >> as per instructions in biomart docs, and try to use this new apache. >> In addition, I would first check perl and may be having an independent >> perl prior to apache + mod_perl installation would be a better test as >> the error you are getting comes from ModPerl. >> >> cheers >> syed >> >> >> On Wed, 2007-09-05 at 12:10 -0400, Mike McCrossin wrote: >>> Hi Syed, >>> >>> I used the default 9002, but in any case, I can see the index page >>> at >>> nurn.informatics.jax.org:9002. But the other two links generate the >>> intenal server error and the same error in the log: >>> >>> [Wed Sep 05 11:57:30 2007] [error] [client xxx.xxx.xxx.202] Use of >>> uninitialized value in concatenation (.) or string at >>> /usr/local/depot/perl-5.8.5/lib/site_perl/5.8.5/sun4-solaris/ModPerl/RegistryCooker.pm >>> line 636.\n >>> >>> Thanks, >>> >>> Mike >>> >>> >>> Syed Haider wrote: >>>> Hi Mike >>>> >>>> could you please >>>> - kill apache. >>>> - set the 'port' in settings.conf to something say : 9001 >>>> - rerun the configure script. >>>> - restart apache. >>>> >>>> and then navigate to http://nurn.informatics.jax.org:9001/ >>>> and see if you see the index page for biomart ? >>>> >>>> After this navigate to >>>> http://nurn.informatics.jax.org:9001/biomart/martservice?type=registry >>>> >>>> and send me what you get back? >>>> >>>> also test if now your >>>> http://nurn.informatics.jax.org:9001/biomart/martview >>>> works or not ? >>>> >>>> >>>> >>>> cheers >>>> syed >>>> >>>> >>>> >>>> On Wed, 2007-09-05 at 11:33 -0400, Mike McCrossin wrote: >>>>> nurn.informatics.jax.org >> > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
