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.
======================================
