Hi I was also looking at a similar discussion board. Its a MP2 isssue. http://www.mail-archive.com/[EMAIL PROTECTED]/msg05761.html
Mirjam, can you find a fix for your system on one of these discussions ? cheers syed On Thu, 2008-07-03 at 15:26 +0100, Richard Holland wrote: > Your mod_perl is so new that BioMart doesn't use the latest config settings. > > This post explains what changed between two recent versions of mod_perl: > > http://mail-archives.apache.org/mod_mbox/perl-dev/200312.mbox/[EMAIL > PROTECTED] > > Syed - you might need to alter the default config file to cope with > this, and/or provide advice to people using the latest mod_perl as to > how to fix the auto-generated configs to cope with the change. > > cheers, > Richard > > 2008/7/3 Mirjam van den Hout - van Vroonhoven <[EMAIL PROTECTED]>: > > Dear all, > > > > > > I'm trying to install biomart on a Redhat AS4 server, but apache fails > > to start with the error message: > > > > [EMAIL PROTECTED] biomart-perl]$ /usr/sbin/httpd -d $PWD -f > > $PWD/conf/httpd.conf > > > > Processing Cached Registry: > > /usr/local/biomart/biomart-perl/conf/cachedRegistries/registryURLPointer.xml.cached > > > > failed to resolve handler Apache::PerlSections > > > > [EMAIL PROTECTED] biomart-perl]$ > > > > > > I am using the RedHat default rpms for apache and mod_perl > > httpd-2.0.52-38.ent.2-x86_64 > > mod_perl-1.99_16-4.5-x86_64 > > These are already running nicely on port 80 (as user apache), serving > > some other content. I want biomart to run on port 8000, as user > > biomart. > > > > I followed all the instructions carefully, installed a bunch of perl > > modules, as instructed by configure.pl. I edited the settings.conf file > > to have apache listen for biomart on port 8000, the first couple of > > lines now read: > > > > [httpdSettings] > > apacheBinary=/usr/sbin/httpd > > serverHost=bioinf-intra.erasmusmc.nl > > port=8000 > > > > The output of the biomart configuration is: > > > > [EMAIL PROTECTED] biomart-perl]$ perl bin/configure.pl -r > > conf/registryURLPointer.xml > > > > Do you want to install in API only mode [y/n] [n]: > > > > Checking prerequisites ...[Looks good] > > Subroutine BioMart::Web::Zlib::adler32 redefined at > > /usr/lib/perl5/5.8.5/Exporter.pm line 65. > > at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 > > Subroutine BioMart::Web::Zlib::crc32 redefined at > > /usr/lib/perl5/5.8.5/Exporter.pm line 65. > > at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 > > Subroutine BioMart::Web::Zlib::MAX_MEM_LEVEL redefined at > > /usr/lib/perl5/5.8.5/Exporter.pm line 65. > > at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 > > Subroutine BioMart::Web::Zlib::MAX_WBITS redefined at > > /usr/lib/perl5/5.8.5/Exporter.pm line 65. > > at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 > > Subroutine BioMart::Web::Zlib::Z_DEFAULT_COMPRESSION redefined at > > /usr/lib/perl5/5.8.5/Exporter.pm line 65. > > at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 > > Subroutine BioMart::Web::Zlib::Z_DEFAULT_STRATEGY redefined at > > /usr/lib/perl5/5.8.5/Exporter.pm line 65. > > at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 > > Subroutine BioMart::Web::Zlib::Z_DEFLATED redefined at > > /usr/lib/perl5/5.8.5/Exporter.pm line 65. > > at /usr/local/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm line 20 > > > > APACHE: /usr/sbin/httpd > > HOST: bioinf-intra.erasmusmc.nl > > PORT: 8000 > > PROXY: > > LOCATION: biomart > > > > You can change the above configuration by editing > > "biomart-perl/conf/settings.conf" > > > > > > > > Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl > > configuration > > Have Apache DSO-support and ModPerl library file present, configuring > > ModPerl in httpd.conf. > > Libdir /usr/local/biomart/biomart-perl/lib is not in @INC, adding to @INC > > > > Cached Registry Unavailable... > > > > Running Complete Clean... > > > > Connection parameters of [MSD PROTOTYPE (EBI)] [ OK ] > > Connection parameters of [UNIPROT PROTOTYPE (EBI)] [ OK ] > > > > > > > > mkdir /usr/local/biomart/biomart-perl/conf/Cached > > mkdir /usr/local/biomart/biomart-perl/conf/Cached/default > > mkdir /usr/local/biomart/biomart-perl/conf/Cached/default/confTrees > > mkdir /usr/local/biomart/biomart-perl/conf/Cached/default/_portables > > mkdir /usr/local/biomart/biomart-perl/conf/Cached/default/XML > > > > [NEW CONFIGURATION] .... WITH MEMORY [default] > > default ... MSD PROTOTYPE (EBI) ...... 001/001 ... msd > > ....................................... (WEB) www.biomart.org:80 > > ............ -> upgrading to 0.6/0.7 ... OK > > default ... UNIPROT PROTOTYPE (EBI) .. 001/006 ... uniprot_location > > .......................... (WEB) www.biomart.org:80 ............ -> > > upgrading to 0.6/0.7 ... OK > > default ... UNIPROT PROTOTYPE (EBI) .. 002/006 ... uniprot_sequence > > .......................... (WEB) www.biomart.org:80 ............ -> > > upgrading to 0.6/0.7 ... OK > > default ... UNIPROT PROTOTYPE (EBI) .. 003/006 ... uniprot_cell_component > > .................... (WEB) www.biomart.org:80 ............ -> upgrading to > > 0.6/0.7 ... OK > > default ... UNIPROT PROTOTYPE (EBI) .. 004/006 ... uniprot_biol_process > > ...................... (WEB) www.biomart.org:80 ............ -> upgrading > > to 0.6/0.7 ... OK > > default ... UNIPROT PROTOTYPE (EBI) .. 005/006 ... uniprot > > ................................... (WEB) www.biomart.org:80 ............ -> > > upgrading to 0.6/0.7 ... OK > > default ... UNIPROT PROTOTYPE (EBI) .. 006/006 ... uniprot_mol_function > > ...................... (WEB) www.biomart.org:80 ............ -> upgrading > > to 0.6/0.7 ... OK > > Setting possible links between datasets > > ....(scanning) 100% > > ....(linking) 100% > > ....(sorting) 100% > > ....(clustering) 7/7 > > ....(resolving) 100% > > Building templates for visible datasets > > .... 100% > > Compiling templates for visible datasets > > [1/2] Attribute Panel of Dataset.. :msd > > [1/2] Filter Panel of Dataset..... :msd > > [2/2] Attribute Panel of Dataset.. :uniprot > > [2/2] Filter Panel of Dataset..... :uniprot > > > > [EMAIL PROTECTED] biomart-perl]$ > > > > Any help will be appreciated! > > > > > > Kind regards, > > > > > > Mirjam van den Hout > > -- > > Dr. Mirjam van den Hout - van Vroonhoven > > system administrator/programmer, dept. of Bioinformatics > > Erasmus Medical Center, Rotterdam, The Netherlands > > Room Number Ee 15.32, phone +31-10-703 81 11 > > Web: http://www.erasmusmc.nl/bioinformatics/ > > E-mail: [EMAIL PROTECTED] > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
