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
