Hi Li, a- which martj version you are using ?
b- could you do 'Save All' from martEditor and send me all the XML files. c- could you check your database for tables like 'meta%' and see if you have any data in them, please confirm. syed On Sun, 2008-04-06 at 12:12 -0400, Li Jin wrote: > Hi, Arek and biomart developers, > > When I install biomart0.6, I got the problem as > ERROR something wrong with your registry: could not load module > BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC > > Anybody can help me? I saw the similiar problem discussed before > http://osdir.com/ml/science.biology.biomart.general/2006-12/msg00014.html. > But I still could not figure it out myself. > > Thanks, > Li > > Here is my myRegistry.xml: > > <?xml version="1.0" encoding="UTF-8"?> > <!DOCTYPE MartRegistry> > <MartRegistry> > > <virtualSchema name="default" visible="0" default="1"> > <MartDBLocation > name = "example" > displayName = "example" > databaseType = "mysql" > host = "localhost" > port = "3306" > database = "mydataset" > schema = "mydataset" > user = "lanfei" > password = "lanfei" > visible = "1" > default = "" > includeDatasets = "" > /> > </virtualSchema> > </MartRegistry> > > The following is the problem in detail: > > [EMAIL PROTECTED] biomart-perl]# perl bin/configure.pl -r > conf/myRegistry.xml > > Do you want to install in API only mode [y/n] [n]: > > Checking prerequisites ...[Looks good] > > APACHE: /usr/local/apache/bin/httpd > HOST: biomart.hljnys.com > PORT: 80 > PROXY: > LOCATION: > > 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 > Have Apache DSO-support and ModPerl library file present, configuring > ModPerl in httpd.conf. > Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC > Libdir /home/lanfei/biomart-perl/lib is not in @INC, adding to @INC > > Cached Registry Unavailable... > > Running Complete Clean... > > > Optional setting for martUser in MartDBLocation location:example not > defined - setting to default values > > Connection parameters of [example] [ OK ] > > Use of uninitialized value in sprintf at > /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1173. > > ERROR something wrong with your registry: could not load module > BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC (@INC > contains: /home/lanfei/biomart-perl/bin/../lib > /usr/local/lib/perl5/site_perl/auto > /root/installserver/2bio-perl/bioperl-live > /usr/local/lib/perl5/5.8.8/i686-linux /usr/local/lib/perl5/5.8.8 > /usr/local/lib/perl5/site_perl/5.8.8/i686-linux > /usr/local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl .) at > (eval 118) line 3. > > > Trace begun at /home/lanfei/biomart-perl/bin/../lib/BioMart/Root.pm line > 169 > BioMart::Root::loadModule('BioMart::Initializer=HASH(0x9e40658)', > 'BioMart::Dataset::') called at > /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1176 > BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x9e40658)') > > called at /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line > 244 > BioMart::Initializer::_init('BioMart::Initializer=HASH(0x9e40658)', > 'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', > 'cached', 'mode', 'memory') called at > /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393 > BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x9e40658)', > 'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', > 'cached', 'mode', 'memory') called at > /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 344 > BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x9e40658)', > 'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', > 'cached', 'mode', 'memory') called at > /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 184 > BioMart::Initializer::_new('BioMart::Initializer=HASH(0x9e40658)', > 'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', > 'cached', 'mode', 'memory') called at > /home/lanfei/biomart-perl/bin/../lib/BioMart/RootI.pm line 42 > BioMart::RootI::new('BioMart::Initializer', 'registryFile', > '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', 'cached', > 'mode', 'memory') called at > /home/lanfei/biomart-perl/bin/configureBioMart.pl line 302 > eval {...} at /home/lanfei/biomart-perl/bin/configureBioMart.pl line 301 >
