Hi, I successfully am running a biomart 0.5 on a Ubuntu Dapper, for various reasons I am consolidating several sites and would like to migrate martview, too.
The target will be a Ubuntu Heron.
I tried simply copying the httpd.conf,
pointing to the NFS mounted biomart-perl.
Upon startup I get
Syntax error on line 13 of /etc/apache2/sites-enabled/030-biomart:
Can't call method "settingsParams" on an undefined value at
/vol/methouse/biomart-perl/lib/BioMart/Initializer.pm line 639.\n
The troubleshooting guide mentions that this might be related
to the mod_perl installation, but I followed
https://bugs.launchpad.net/ubuntu/+source/libapache2-mod-perl2/+bug/55464
and indeed a simple test.pl can be seen in the browser.
If I copy the <perl> ... </perl> snippet from httpd.conf
into a new file test.pl, I can run it as www-data without problems.
If I try to re-generate the configuration, I get the error below.
One curious thing is that it won't find a dataset name
BioMart::Dataset::: Can't locate BioMart/Dataset/.pm
Indeed, the includeDatasets is empty in my registry,
but it works on the other installation ?!
I can also see the cached configuration if I start apache
on the other host:
biomart-perl/conf/Cached/default/XML/msbi_mart_1.litlist.default
biomart-perl/conf/Cached/default/XML/msbi_mart_1.xcms.default
My working assumption is that one of the dependencies is too new
in Heron, so I am happy to take advice which that might be,
and how to continue debugging. I also checked the postgres access,
and that _seems_ to be working.
Yours,
Steffen
-------------------------------------------------
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation
name = "msbi_mart_1"
displayName = "MSBI Metabolites"
databaseType = "postgres"
host = "kons"
port = "5432"
database = "biomart"
schema = "public"
user = "biomart"
password = "XXX"
visible = "1"
default = ""
includeDatasets = ""
martUser = ""
/>
</MartRegistry>
-------------------------------------------------
perl bin/configure.pl --clean -r conf/defaultMartRegistry.xml
Do you want to install in API only mode [y/n] [n]:
Checking prerequisites ...[Looks good]
DO YOU WANT TO USE EXISTING SERVER CONFIGURATION [y/n] [y]: n
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:
/usr/sbin/apache2
[1]:
Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl
configuration
Have Apache DSO-support and ModPerl library file present, configuring ModPerl
in httpd.conf.
Enter the server host OR default [msbi]:
Enter the server port OR default [5555]:
Enter proxy OR default :
Enter the required script location OR default [biomart]:
Libdir /vol/methouse/biomart-perl/lib is not in @INC, adding to @INC
Use of uninitialized value in sprintf at
/vol/methouse/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:
/vol/methouse/biomart-perl/bin/../lib /etc/perl /usr/local/lib/perl/5.8.8
/usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8
/usr/share/perl/5.8 /usr/local/lib/site_perl .) at (eval 145) line 3.
Trace begun at /vol/methouse/biomart-perl/bin/../lib/BioMart/Root.pm line 169
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x23fac00)',
'BioMart::Dataset::') called at
/vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line 1187
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x23fac00)')
called at /vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line 244
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x23fac00)',
'registryFile', '/vol/methouse/biomart-perl/conf/defaultMartRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line 393
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x23fac00)',
'registryFile', '/vol/methouse/biomart-perl/conf/defaultMartRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/vol/methouse/biomart-perl/bin/../lib/BioMart/Initializer.pm line 160
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x23fac00)',
'registryFile', '/vol/methouse/biomart-perl/conf/defaultMartRegistry.xml',
'action', 'clean', 'mode', 'memory') called at
/vol/methouse/biomart-perl/bin/../lib/BioMart/RootI.pm line 42
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'/vol/methouse/biomart-perl/conf/defaultMartRegistry.xml', 'action', 'clean',
'mode', 'memory') called at /vol/methouse/biomart-perl/bin/configureBioMart.pl
line 339
eval {...} at /vol/methouse/biomart-perl/bin/configureBioMart.pl line 338
--
IPB Halle AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann http://www.IPB-Halle.DE
Weinberg 3 http://msbi.bic-gh.de
06120 Halle Tel. +49 (0) 345 5582 - 1470
+49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
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