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.
> ======================================
>
>
