Hi all,
I am still having trouble connecting to the database (I checked out
the most recent biomart-perl). I ran MartEditor and exporter the naive
settings (got all meta-tables)
Syed, the myRegistry.xml I sent you is still up-to-date, in case you
want to check again.
/usr/sbin/httpd -d $PWD -f
/home/juettemann/biomart/biomart-perl/conf/httpd.conf
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
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Syntax error on line 44 of
/home/juettemann/biomart/biomart-perl/conf/httpd.conf:
8\xe9c\t\x01
httpd.conf:
42 LoadModule authz_host_module
/usr/lib/httpd/modules/mod_authz_host.so
43 <Perl>
44 use lib
'/home/juettemann/biomart/biomart-perl/lib';
45 require "BioMart/Web/SiteDefs.pm";
I tried to remove all whitespaces preceeding/trailing from line 44,
just in case something hidden in there.
[bischet] ~/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]
APACHE: /usr/sbin/httpd
HOST: localhost
PORT: 80
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
Libdir /home/juettemann/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
/home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 254
BioMart::Initializer::_init('BioMart::Initializer=HASH(0xb227ea4)',
'registryFile',
'/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0xb227ea4)',
'registryFile',
'/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 328
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0xb227ea4)',
'registryFile',
'/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/Initializer.pm
line 168
BioMart::Initializer::_new('BioMart::Initializer=HASH(0xb227ea4)',
'registryFile',
'/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/juettemann/biomart/biomart-perl/bin/../lib/BioMart/RootI.pm line
64
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/juettemann/biomart/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/juettemann/biomart/biomart-perl/bin/configureBioMart.pl line 328
eval {...} at /home/juettemann/biomart/biomart-perl/bin/configureBioMart.pl
line 327
Cheers,
Thomas
