On 8 Dec 2006, at 10:08, Hermida, Leandro wrote:
Hello,
I have installed and attempted to configure BioMart 0.5 and I am
running
into a few problems:
1) When attempting to run the configure script for the first time, I
run
into the following error:
------------------------------------------
[EMAIL PROTECTED]:~/current/biomart-perl> perl bin/configure.pl -r
conf/registryURLPointer.xml
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
Checking several common Apache locations...done.
Select either one of the detected httpd paths on the list, OR enter the
path you wish to use:
[No plausible httpd binaries found]
[1]: /home/biomart/apache/bin/httpd
Got usable Apache in /home/biomart/apache/bin/httpd, probing for
version
& ModPerl configuration
Have ModPerl statically compiled into httpd, configuring ModPerl in
httpd.conf.
Enter the server host OR default [server]:
Enter the server port OR default [5555]:
Enter proxy OR default :
Enter the required script location OR default [biomart]:
Libdir /home/biomart/0.5/biomart-perl/lib is not in @INC, adding to
@INC
Cached Registry Unavailable...
Running Complete Clean...
ERROR something wrong with your registry:
syntax error at line 1, column 0, byte 0 at
/usr/lib/perl5/vendor_perl/5.8.3/x86_64-linux-thread-multi/XML/
Parser.pm
line 187
Hi Leandro,
This is one of the bugs we have fixed recently.
Can you throw away the old code do a clean checkout from cvs
and try again and see if the error persist? It should work now
If not, drop us a line and we'll investigate
(you can also try registryDBPointer.xml - this should not be affected
in any case)
but this requires an open outgoing connection on 3306
a.
[EMAIL PROTECTED]:~/current/biomart-perl>
--------------------------------------------
This error usually would pop up if there was a problem with the XML
file
but I cannot find any problem with registryURLPointer.xml which came
from your distribution.
2) When attempting to use my own Registry XML file I get this error:
---------------------------------------------
[EMAIL PROTECTED]:~/current/biomart-perl> perl bin/configure.pl --clean -r
conf/myRegistry.xml
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
rm /home/biomart/0.5/biomart-perl/conf/templates/default/*.ttcrm:
cannot
remove `/home/biomart/0.5/biomart-perl/conf/templates/default/*.ttc':
No
such file or directory
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]:
Use of uninitialized value in sprintf at
/home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
1184.
ERROR something wrong with your registry: could not load module
BioMart::Dataset::: Can't locate BioMart/Dataset/.pm in @INC (@INC
contains: /home/biomart/0.5/biomart-perl/bin/../lib
/usr/lib/perl5/5.8.3/x86_64-linux-thread-multi /usr/lib/perl5/5.8.3
/usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.3/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.3 /usr/lib/perl5/vendor_perl .) at (eval
145) line 3.
Trace begun at
/home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Root.pm
line 169
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x2160910)',
'BioMart::Dataset::') called at
/home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
1187
BioMart::Initializer::_populateRegistry('BioMart::
Initializer=HASH(0x216
0910)') called at
/home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
244
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x2160910)',
'registryFile', '/home/biomart/0.5/biomart-perl/conf/myRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
393
BioMart::Initializer::init_clean('BioMart::
Initializer=HASH(0x2160910)',
'registryFile', '/home/biomart/0.5/biomart-perl/conf/myRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/biomart/0.5/biomart-perl/bin/../lib/BioMart/Initializer.pm line
160
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x2160910)',
'registryFile', '/home/biomart/0.5/biomart-perl/conf/myRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/home/biomart/0.5/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/home/biomart/0.5/biomart-perl/conf/myRegistry.xml', 'action',
'clean',
'mode', 'memory') called at
/home/biomart/0.5/biomart-perl/bin/configureBioMart.pl line 339
eval {...} at /home/biomart/0.5/biomart-perl/bin/configureBioMart.pl
line 338
[EMAIL PROTECTED]:~/current/biomart-perl>
-----------------------------------------------------
3) I cannot get martbuilder to run. I get the following error:
[EMAIL PROTECTED]:~current/martj> bin/martbuilder.sh
Starting MartBuilder please wait ....
Exception in thread "main" java.lang.NoClassDefFoundError:
org/apache/log4j/Appender
at
org.biomart.common.resources.Settings.setApplication(Settings.java:99)
at
org.biomart.builder.view.gui.MartBuilder.main(MartBuilder.java:58)
[EMAIL PROTECTED]:~/current/martj>
------------------------------------------------------------------------
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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