Hi! I am having trouble creating a mart with biomart ver 0.6 Although I'm able to build my main and dimension tables (although I tried also just a single main table) with martbuilder - when I run marteditor, create a naive configuration and then try to export it to the mart schema - it seems to get stuck at some point, although without error messages. I'm assuming it gets stuck because 4 out of the 6 meta% tables have no data in it and I checked other mart dumps, and there was something in each of it (only meta_template__xml__dm and meta_version__version__main have an entry). I'm not sure when are the rest of the meta% tables supposed to be populated, but perl bin/configure.pl -r conf/myRegistry.xml fails - and it seems that's because of the fact that the table meta_conf__dataset__main doesn't have any rows.
Here are the technical details: - for database, I tried Oracle 10g 10.2.0.3 and Mysql 4.1.10a - for java, I tried 'Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_09-b03)' on Fedora Core release 4 (Stentz) (kernel:2.6.13-1.1532_FC4smp, architecture:x86_64) also 'Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_11-b03)' on Fedora Core release 3 (Heidelberg) (kernel:2.6.9-1.667smp, architecture:i686) This is what I see on the standard output when I run export: created template tables created meta tables SELECT dataset_id_key FROM MAPPING_MART.meta_conf__dataset__main where dataset='MAPPING' and type='TableSet' and display_name='MAPPING' DELETE FROM MAPPING_MART.meta_conf__user__dm WHERE dataset_id_key=1 INSERT INTO MAPPING_MART.meta_conf__user__dm VALUES (1,'default') DELETE FROM MAPPING_MART.meta_conf__interface__dm WHERE dataset_id_key=1 DELETE FROM MAPPING_MART.meta_conf__interface__dm WHERE dataset_id_key=1 select count(*) from MAPPING_MART.meta_conf__dataset__main where dataset_id_key = ? Then, when I try "perl bin/configure.pl --clean -r conf/myRegistry.xml", I get: Connection parameters of [My Example] [ OK ] Use of uninitialized value in sprintf at /usr/local/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 Changing the database to mysql, or the linux architecture, or the java runtime (I even tried 1.4.2_08) doesn't change anything in the above behavior. I have also tried a single main table - no luck. Can someone explain what I'm doing wrong? I am trying to debug now marteditor (I checked out the source) - but it might take a while before I get to the meta% table population SQL clauses). Thank you, Razvan
begin:vcard fn:Razvan Sultana n:Sultana;Razvan org:Dana-Farber Cancer Institute;Biostatistics and Computational Biology adr;dom:;;44 Binney St;Boston;MA;02115 email;internet:[EMAIL PROTECTED] title:Bioinformatics Engineer tel;work:617-632-6773 x-mozilla-html:FALSE url:http://compbio.dfci.harvard.edu/tgi version:2.1 end:vcard
