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] >
