Hi Thomas,
it looks ok already.
now the problem seems to be with your connection parameters in you
registry.
I would first try and configure with the registry martDBLocation.xml
cheers
syed
On Wed, 2008-07-09 at 16:27 -0700, Thomas Juettemann wrote:
> Hi Syed,
>
> many thanks for the answer.
>
> I check for the modules, I could not find any problems. I checked for
> the version, all have 2.011, I also used them in a script, no error
> from Perl.
> Do you want me to run a specific test?
>
> apxs2 is now installed
>
> just in case, the updated error:
>
> Do you want to install in API only mode [y/n] [n]:
>
> Checking prerequisites ...[Looks good]
>
> APACHE: /usr/sbin/httpd
> HOST: localhost
> PORT: 9002
> PROXY:
> LOCATION: biomart
>
> You can change the above configuration by editing
> "biomart-perl/conf/settings.conf"
>
> Got usable Apache in /usr/sbin/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
>
> Cached Registry Unavailable...
>
> Running Complete Clean...
>
> Optional setting for martUser in MartDBLocation location:bischet not
> defined - setting to default values
>
>
>
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
> COULD NOT CONNECT TO DATABASE pdb.CHECK YOUR SETTINGS
>
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
>
>
>
> 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
> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 254
> BioMart::Initializer::_init('BioMart::Initializer=HASH(0xa9348b8)',
> 'registryFile',
> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 377
> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xa9348b8)',
> 'registryFile',
> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 328
> BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xa9348b8)',
> 'registryFile',
> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> line 168
> BioMart::Initializer::_new('BioMart::Initializer=HASH(0xa9348b8)',
> 'registryFile',
> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm
> line 64
> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> 'action', 'cached', 'mode', 'memory') called at
> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> line 328
> eval {...} at
> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> line 327
>
>
>
>
> On Wed, Jul 9, 2008 at 15:48, Syed Haider <[EMAIL PROTECTED]> wrote:
> > Thomas,
> > please test if the following CPAN modules are functional and do not
> > have broken or multiple installations:
> >
> > Compress::Zlib;
> > Compress::Raw::Zlib;
> > IO::Compress::Gzip;
> >
> >
> > Furthermore, you need to get apxs or apxs2. For details please see docs.
> >
> > cheers
> > syed
> >
> >
> > On Wed, 2008-07-09 at 14:13 -0700, Thomas Juettemann wrote:
> >> Dear all,
> >>
> >> I am failing at the very begining, when running configure.pl:
> >>
> >> [camano] ~/compbio/programs/biomart/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]
> >> Subroutine BioMart::Web::Zlib::adler32 redefined at
> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> line 20
> >> Subroutine BioMart::Web::Zlib::crc32 redefined at
> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> line 20
> >> Subroutine BioMart::Web::Zlib::ZLIB_VERNUM redefined at
> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> line 20
> >> Subroutine BioMart::Web::Zlib::MAX_MEM_LEVEL redefined at
> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> line 20
> >> Subroutine BioMart::Web::Zlib::MAX_WBITS redefined at
> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> line 20
> >> Subroutine BioMart::Web::Zlib::Z_DEFAULT_COMPRESSION redefined at
> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> line 20
> >> Subroutine BioMart::Web::Zlib::Z_DEFAULT_STRATEGY redefined at
> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> line 20
> >> Subroutine BioMart::Web::Zlib::Z_DEFLATED redefined at
> >> /usr/lib/perl5/5.8.5//Exporter.pm line 65.
> >> at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Web/Zlib.pm
> >> line 20
> >> Use of uninitialized value in string ne at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> line 110.
> >> Use of uninitialized value in regexp compilation at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> line 112.
> >>
> >> rm
> >> /projects/compbio/programs/biomart/biomart-perl/conf/templates/default/*.ttcrm:
> >> cannot remove
> >> `/projects/compbio/programs/biomart/biomart-perl/conf/templates/default/*.ttc':
> >> No such file or directory
> >>
> >> APACHE: /usr/sbin/httpd
> >> HOST: localhost
> >> PORT: 9002
> >> PROXY:
> >> LOCATION: biomart
> >>
> >> You can change the above configuration by editing
> >> "biomart-perl/conf/settings.conf"
> >>
> >>
> >>
> >> Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl
> >> configuration
> >> Can't exec "/usr/sbin/apxs2": No such file or directory at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> line 173.
> >> Use of uninitialized value in scalar chomp at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> line 174.
> >> Use of uninitialized value in concatenation (.) or string at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> line 176.
> >> Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC
> >> Libdir /projects/compbio/programs/biomart/biomart-perl/lib is not in
> >> @INC, adding to @INC
> >>
> >> Cached Registry Unavailable...
> >>
> >> Running Complete Clean...
> >>
> >>
> >> Optional setting for martUser in MartDBLocation location:bischet not
> >> defined - setting to default values
> >>
> >>
> >>
> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >>
> >> COULD NOT CONNECT TO DATABASE pdb.CHECK YOUR SETTINGS
> >>
> >>
> >> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> >>
> >>
> >> 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
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> line 254
> >> BioMart::Initializer::_init('BioMart::Initializer=HASH(0xb1d3f48)',
> >> 'registryFile',
> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> 'action', 'cached', 'mode', 'memory') called at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> line 377
> >> BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xb1d3f48)',
> >> 'registryFile',
> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> 'action', 'cached', 'mode', 'memory') called at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> line 328
> >> BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xb1d3f48)',
> >> 'registryFile',
> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> 'action', 'cached', 'mode', 'memory') called at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
> >> line 168
> >> BioMart::Initializer::_new('BioMart::Initializer=HASH(0xb1d3f48)',
> >> 'registryFile',
> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> 'action', 'cached', 'mode', 'memory') called at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm
> >> line 64
> >> BioMart::RootI::new('BioMart::Initializer', 'registryFile',
> >> '/projects/compbio/programs/biomart/biomart-perl/conf/myRegistry.xml',
> >> 'action', 'cached', 'mode', 'memory') called at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> line 328
> >> eval {...} at
> >> /projects/compbio/programs/biomart/biomart-perl/bin/configureBioMart.pl
> >> line 327
> >>
> >>
> >> [camano] ~/compbio/programs/biomart/biomart-perl: perl -MXML::Simple
> >> -e 'print "$XML::Simple::VERSION\n"'
> >> 2.18
> >>
> >> Registry with user and password blanked:
> >> [camano] ~/compbio/programs/biomart/biomart-perl: cat conf/myRegistry.xml
> >> <?xml version="1.0" encoding="UTF-8"?>
> >> <!DOCTYPE MartRegistry>
> >> <MartRegistry>
> >> <virtualSchema name = "default">
> >> <MartDBLocation
> >> name = "bischet"
> >> displayName = "BISC-Het"
> >> databaseType = "mysql"
> >> host = "magnet.cse.ucsc.edu"
> >> port = "3306"
> >> database = "pdb"
> >> schema = ""
> >> user = "XXXX"
> >> password = "XXXXX"
> >> visible = "1"
> >> default = ""
> >> includeDatasets = ""
> >> />
> >> </virtualSchema>
> >> </MartRegistry>
> >>
> >> The connection connection works fine from the command line from any
> >> server. I tried it with schema = "pdb" and blank (like in example)
> >> There is no meta_conf table yet
> >>
> >> Any help greatly appreciated!
> >>
> >> Many thanks,
> >> Thomas
> > --
> > ======================================
> > Syed Haider.
> > EMBL-European Bioinformatics Institute
> > Wellcome Trust Genome Campus, Hinxton,
> > Cambridge CB10 1SD, UK.
> > ======================================
> >
> >
--
======================================
Syed Haider.
EMBL-European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
======================================
