Hi Nelson,
Probably the configuration has lost its type setting on the
DatasetConfig node. It should be set to TableSet. Do you see this in
MartEditor? If you can't see it then something may have gone wrong in
the export process - I can come and find you in person and help you
fix it.
Cheers
Damian
On Tue, Oct 12, 2010 at 5:24 PM, Nelson Ndegwa <nnde...@ebi.ac.uk
<mailto:nnde...@ebi.ac.uk>> wrote:
Hi All,
I am having problems reconfiguring my previously working MartView.
I was attempting to link two datasets using two attributes/filters
instead of the usual one attribute/filter using MartEditor.
On trying to revert back to the old configuration after deleting
my changes, i still get the same error (below)
Any ideas?
Thanks,
Nelson
/[biomart-perl]$ perl bin/configure.pl <http://configure.pl>
--clean -r conf/reactomeEwas.xml/
/Do you want to install in API only mode [y/n] [n]: /
/Checking prerequisites ...[Looks good] /
/APACHE: /homes/nn/soft/biomart/apache/bin/httpd/
/HOST: localhost/
/PORT: 9000/
/PROXY:/
/LOCATION: biomart/
/Use of uninitialized value in print at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/configureBioMart.pl
line 147./
/APXS/2:/
/You can change the above configuration by editing
"biomart-perl/conf/settings.conf"/
/Got usable Apache in /homes/nn/soft/biomart/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
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/lib is
not in @INC, adding to @INC/
/Cached Registry Unavailable.../
/Running Complete Clean.../
/Connection parameters of [REACTOME] [ OK ]/
/Connection parameters of [ENSEMBL 44 GENES (SANGER)] [ OK ]/
/Connection parameters of [UNIPROT (EBI UK)] [ OK ]/
/Connection parameters of [PRIDE BioMart] [ OK ]/
/ERROR something wrong with your registry: could not load module
BioMart::Dataset::Problem retrieving datasets for mart uniprot_mart,
check your parameters: syntax error at (eval 131) line 1, near
"require BioMart::Dataset::Problem retrieving datasets "/
/Trace begun at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Root.pm
line 191/
/BioMart::Root::loadModule('BioMart::Initializer=HASH(0x4353ce8)',
'BioMart::Dataset::Problem retrieving datasets for mart
uniprot_mart, check your parameters') called at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 1162/
/BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x4353ce8)')
called at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 228/
/BioMart::Initializer::_init('BioMart::Initializer=HASH(0x4353ce8)',
'registryFile',
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
'action', 'cached', 'mode', 'memory') called at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 377/
/BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x4353ce8)',
'registryFile',
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
'action', 'cached', 'mode', 'memory') called at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 328/
/BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x4353ce8)',
'registryFile',
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
'action', 'cached', 'mode', 'memory') called at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 168/
/BioMart::Initializer::_new('BioMart::Initializer=HASH(0x4353ce8)',
'registryFile',
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
'action', 'cached', 'mode', 'memory') called at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm
line 64/
/BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/conf/reactomeEwas.xml',
'action', 'cached', 'mode', 'memory') called at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/configureBioMart.pl
line 332/
/eval {...} at
/automount/nas10b_vol-vol1-homes/nn/soft/biomart/biomart-perl/bin/configureBioMart.pl
line 331/
/[biomart-perl]$/
