Hi Leandro
Further to my last mail, I can see from your errors that dataset 'type'
which should be 'tableset', and which comes from your xml file and your
Mart's meta_conf__dataset__main type column is missing. Could you have a
look at your mart and xml.
As Arek mentioned that we have recently fixed the registryURLPointer
bug, so it should be working now with updated code, however if it still
doesnt work, then try sending the file I mentioned in the last mail
biomart-perl/conf/registry_DOM_XML. Its generated when the software
fails on registryURLPointer.
Cheers
Syed
On Fri, 2006-12-08 at 11:08 +0100, Hermida, Leandro wrote:
> Hello,
>
> I have installed and attempted to configure BioMart 0.5 and I am running
> into a few problems:
>
> 1) When attempting to run the configure script for the first time, I run
> into the following error:
> ------------------------------------------
> [EMAIL PROTECTED]:~/current/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]
> Checking several common Apache locations...done.
>
> Select either one of the detected httpd paths on the list, OR enter the
> path you wish to use:
> [No plausible httpd binaries found]
> [1]: /home/biomart/apache/bin/httpd
> Got usable Apache in /home/biomart/apache/bin/httpd, probing for version
> & ModPerl configuration
> Have ModPerl statically compiled into httpd, configuring ModPerl in
> httpd.conf.
>
> Enter the server host OR default [server]:
>
> Enter the server port OR default [5555]:
>
> Enter proxy OR default :
>
> Enter the required script location OR default [biomart]:
> Libdir /home/biomart/0.5/biomart-perl/lib is not in @INC, adding to @INC
>
> Cached Registry Unavailable...
>
> Running Complete Clean...
>
> ERROR something wrong with your registry:
> syntax error at line 1, column 0, byte 0 at
> /usr/lib/perl5/vendor_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm
> line 187
>
> [EMAIL PROTECTED]:~/current/biomart-perl>
> --------------------------------------------
> This error usually would pop up if there was a problem with the XML file
> but I cannot find any problem with registryURLPointer.xml which came
> from your distribution.
>
>
>
> 2) When attempting to use my own Registry XML file I get this error:
> ---------------------------------------------
> [EMAIL PROTECTED]:~/current/biomart-perl> perl bin/configure.pl --clean -r
> conf/myRegistry.xml
>
> Do you want to install in API only mode [y/n] [n]:
>
> Checking prerequisites ...[Looks good]
>
> rm /home/biomart/0.5/biomart-perl/conf/templates/default/*.ttcrm: cannot
> remove `/home/biomart/0.5/biomart-perl/conf/templates/default/*.ttc': No
> such file or directory
>
>
> DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]:
>
>
> Use of uninitialized value in sprintf at
> /home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
> 1184.
>
> ERROR something wrong with your registry: could not load module
> BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC (@INC
> contains: /home/biomart/0.5/biomart-perl/bin/../lib
> /usr/lib/perl5/5.8.3/x86_64-linux-thread-multi /usr/lib/perl5/5.8.3
> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl
> /usr/lib/perl5/vendor_perl/5.8.3/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl .) at (eval
> 145) line 3.
>
>
> Trace begun at /home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Root.pm
> line 169
> BioMart::Root::loadModule('BioMart::Initializer=HASH(0x2160910)',
> 'BioMart::Dataset::') called at
> /home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
> 1187
> BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x216
> 0910)') called at
> /home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
> 244
> BioMart::Initializer::_init('BioMart::Initializer=HASH(0x2160910)',
> 'registryFile', '/home/biomart/0.5/biomart-perl/conf/myRegistry.xml',
> 'action', 'clean', 'mode', 'memory') called at
> /home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
> 393
> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x2160910)',
> 'registryFile', '/home/biomart/0.5/biomart-perl/conf/myRegistry.xml',
> 'action', 'clean', 'mode', 'memory') called at
> /home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
> 160
> BioMart::Initializer::_new('BioMart::Initializer=HASH(0x2160910)',
> 'registryFile', '/home/biomart/0.5/biomart-perl/conf/myRegistry.xml',
> 'action', 'clean', 'mode', 'memory') called at
> /home/biomart/0.5/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> '/home/biomart/0.5/biomart-perl/conf/myRegistry.xml', 'action', 'clean',
> 'mode', 'memory') called at
> /home/biomart/0.5/biomart-perl/bin/configureBioMart.pl line 339
> eval {...} at /home/biomart/0.5/biomart-perl/bin/configureBioMart.pl
> line 338
>
> [EMAIL PROTECTED]:~/current/biomart-perl>
> -----------------------------------------------------
>
> 3) I cannot get martbuilder to run. I get the following error:
>
> [EMAIL PROTECTED]:~current/martj> bin/martbuilder.sh
> Starting MartBuilder please wait ....
> Exception in thread "main" java.lang.NoClassDefFoundError:
> org/apache/log4j/Appender
> at
> org.biomart.common.resources.Settings.setApplication(Settings.java:99)
> at
> org.biomart.builder.view.gui.MartBuilder.main(MartBuilder.java:58)
> [EMAIL PROTECTED]:~/current/martj>
>
>
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
