Hi, Syed,
a. I did not use martj for configuration. I modify the myRegistry.xml
manually. Sould I have to use martj?
b. I did not use martEditor. SHould I have to use martEditor?
c. I have the following meta* tables in database:
meta_conf__dataset__main |
| meta_conf__interface__dm |
| meta_conf__user__dm |
| meta_conf__xml__dm |
| meta_configuration |
| meta_interface |
| meta_user |
| meta_version__version__main |
mysql> select * from meta_conf__dataset__main;
+----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+
| dataset_id_key | dataset | display_name | description | type
| visible | version | modified |
+----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+
| 1 | msd | MSD | protein structures | TableSet
| 1 | 15-2005_07_28 | 20060124143506 |
+----------------+---------+--------------+---------------------+----------+---------+---------------+----------------+
1 row in set (0.00 sec)
mysql> select * from meta_conf__interface__dm;
Empty set (0.02 sec)
mysql> select * from meta_conf__user__dm ;
+----------------+-----------+
| dataset_id_key | mart_user |
+----------------+-----------+
| 1 | default |
+----------------+-----------+
1 row in set (0.04 sec)
mysql> select * from meta_conf__xml__dm ;
Empty set (0.02 sec)
mysql> select * from meta_configuration ;
Empty set (0.00 sec)
mysql> select * from meta_interface ;
Empty set (0.06 sec)
mysql> select * from meta_configuration ;
Empty set (0.00 sec)
mysql> select * from meta_version__version__main;
Empty set (0.03 sec)
Thank you!
--Li
On Sun, 6 Apr 2008, Syed Haider wrote:
Hi Li,
a- which martj version you are using ?
b- could you do 'Save All' from martEditor and send me all the XML
files.
c- could you check your database for tables like 'meta%' and see if you
have any data in them, please confirm.
syed
On Sun, 2008-04-06 at 12:12 -0400, Li Jin wrote:
Hi, Arek and biomart developers,
When I install biomart0.6, I got the problem as
ERROR something wrong with your registry: could not load module
BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC
Anybody can help me? I saw the similiar problem discussed before
http://osdir.com/ml/science.biology.biomart.general/2006-12/msg00014.html.
But I still could not figure it out myself.
Thanks,
Li
Here is my myRegistry.xml:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<virtualSchema name="default" visible="0" default="1">
<MartDBLocation
name = "example"
displayName = "example"
databaseType = "mysql"
host = "localhost"
port = "3306"
database = "mydataset"
schema = "mydataset"
user = "lanfei"
password = "lanfei"
visible = "1"
default = ""
includeDatasets = ""
/>
</virtualSchema>
</MartRegistry>
The following is the problem in detail:
[EMAIL PROTECTED] 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/local/apache/bin/httpd
HOST: biomart.hljnys.com
PORT: 80
PROXY:
LOCATION:
You can change the above configuration by editing
"biomart-perl/conf/settings.conf"
Got usable Apache in /usr/local/apache/bin/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/lanfei/biomart-perl/lib is not in @INC, adding to @INC
Cached Registry Unavailable...
Running Complete Clean...
Optional setting for martUser in MartDBLocation location:example not
defined - setting to default values
Connection parameters of [example] [ OK ]
Use of uninitialized value in sprintf at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1173.
ERROR something wrong with your registry: could not load module
BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC (@INC
contains: /home/lanfei/biomart-perl/bin/../lib
/usr/local/lib/perl5/site_perl/auto
/root/installserver/2bio-perl/bioperl-live
/usr/local/lib/perl5/5.8.8/i686-linux /usr/local/lib/perl5/5.8.8
/usr/local/lib/perl5/site_perl/5.8.8/i686-linux
/usr/local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl .) at
(eval 118) line 3.
Trace begun at /home/lanfei/biomart-perl/bin/../lib/BioMart/Root.pm line
169
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x9e40658)',
'BioMart::Dataset::') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1176
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x9e40658)')
called at /home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line
244
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x9e40658)',
'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x9e40658)',
'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 344
BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x9e40658)',
'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/Initializer.pm line 184
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x9e40658)',
'registryFile', '/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action',
'cached', 'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/lanfei/biomart-perl/conf/myRegistry.xml', 'action', 'cached',
'mode', 'memory') called at
/home/lanfei/biomart-perl/bin/configureBioMart.pl line 302
eval {...} at /home/lanfei/biomart-perl/bin/configureBioMart.pl line 301
