Hi Ray, Thanks for sending us the registry.
Since you are first time biomart user, I do not encourage you use 'RegistryURLPointer' in your registry file. Rather, please use one of the registry examples under 'conf' directory, for example, martDBLocation.xml. After you run bin/configure.pl with this registry file successfully, then you know the installation is OK. Let us know how it goes. Kind regards, Junjun > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Jing, Rui > Sent: Thursday, October 29, 2009 9:46 AM > To: Jianxin Wang; [email protected] > Subject: RE: [mart-dev] The problem with Biomart installation > - need your help > > Hi Jason, > > Here is my registryuRLPointer.xml > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE MartRegistry> > <MartRegistry> > <RegistryURLPointer > name = "central_server" > host = "promoter.dfci.harvard.edu" > port = "80" > path = "" > includeMarts = "msd,uniprot" > /> > </MartRegistry> > > Thanks, > > Rui > > ________________________________ > > From: Jianxin Wang [mailto:[email protected]] > Sent: Wed 10/28/2009 6:40 PM > To: Jing, Rui; [email protected] > Subject: RE: [mart-dev] The problem with Biomart installation > - need your help > > > > 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(0x > cf381e0)', > '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(0 > xcf381e0)', > '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/TemplateBui > lder.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. > > > > > >
