Hi Ray,
The error message (I listed it again below) is actually very informative. It
seems like in your registry, there was a mart you use URLLocation, but the
setting had problem, hence: "Problems with the web server: 404 Not Found".
Please verify all the settings are correct in your registry.
Good luck,
Junjun
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)
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of Jing, Rui
> Sent: Wednesday, October 28, 2009 4:03 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
>
>
>
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