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 --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]$/
