Hi Jing, Could you send us your registry.xml file? In your case the "registryuRLPointer.xml"?
Jason ________________________________________ From: [email protected] [[email protected]] On Behalf Of Jing, Rui [[email protected]] Sent: Wednesday, October 28, 2009 4:02 PM To: [email protected] Subject: RE: [mart-dev] The problem with Biomart installation - need your help Hi, I am trying to install Biomart. When running perl bin/configure.pl -r conf/registryURLPointer.xml I get the following error message: Checking prerequisites ...[Looks good] Use of uninitialized value in string ne at /home/software/biomart-perl/bin/configureBioMart.pl line 110. Use of uninitialized value in regexp compilation at /home/software/biomart-perl/bin/configureBioMart.pl line 112. rm /home/software/biomart-perl/conf/templates/default/*.ttcrm: cannot remove `/home/software/biomart-perl/conf/templates/default/*.ttc': No such file or directory APACHE: /usr/local/apache/bin/httpd HOST: promoter PORT: 80 PROXY: LOCATION: biomart-perl APXS/2: You can change the above configuration by editing "biomart-perl/conf/settings.conf" Got usable Apache in /usr/local/apache/bin/httpd, probing for version & ModPerl configuration Libdir /home/software/biomart-perl/lib is not in @INC, adding to @INC Cached Registry Unavailable... Running Complete Clean... Problems with the web server: 404 Not Found ERROR something wrong with your registry: Problems with the retrieval of dataset configuration Please check: that your mart Registry files contains correct connection params, that you are using the correct version on XML::Simple, that BioMart databases contain a populated meta_conf tables and that you have set martUser correctly if you are running in restricted data access mode (populated meta_conf__user__dm) Trace begun at /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 254 BioMart::Initializer::_init('BioMart::Initializer=HASH(0xcf381e0)', 'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 377 BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xcf381e0)', 'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 328 BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xcf381e0)', 'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/software/biomart-perl/bin/../lib/BioMart/Initializer.pm line 168 BioMart::Initializer::_new('BioMart::Initializer=HASH(0xcf381e0)', 'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/software/biomart-perl/bin/../lib/BioMart/RootI.pm line 64 BioMart::RootI::new('BioMart::Initializer', 'registryFile', '/home/software/biomart-perl/conf/registryURLPointer.xml', 'action', 'cached', 'mode', 'memory') called at /home/software/biomart-perl/bin/configureBioMart.pl line 331 eval {...} at /home/software/biomart-perl/bin/configureBioMart.pl line 330 thanks, Ray ________________________________ From: [email protected] on behalf of Jing, Rui Sent: Wed 10/28/2009 2:10 PM To: [email protected] Subject: [mart-dev] The problem with Biomart installation - need your help Hi I am trying to install Biomart. When running perl bin/configure.pl -r conf/registryURLPointer.xml I get the following error message: Checking prerequisites ...[Looks good] Can't locate XML/Simple.pm in @INC (@INC contains: /home/software/biomart-perl/bin/../lib /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.8.7/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.8.6/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl/5.8.7 /usr/lib/perl5/site_perl/5.8.6 /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.8.7/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.8.6/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl/5.8.6 /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /home/software/biomart-perl/bin/../lib/BioMart/Web.pm line 48. BEGIN failed--compilation aborted at /home/software/biomart-perl/bin/../lib/BioMart/Web.pm line 48. Compilation failed in require at (eval 15) line 3. ...propagated at /usr/lib/perl5/5.8.8/base.pm line 85. BEGIN failed--compilation aborted at /home/software/biomart-perl/bin/../lib/BioMart/Web/TemplateBuilder.pm line 53. Compilation failed in require at /home/software/biomart-perl/bin/configureBioMart.pl line 39. BEGIN failed--compilation aborted at /home/software/biomart-perl/bin/configureBioMart.pl line 39. Please would you be able to tell me how to fix this? Thanks Ray The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
