[Gmod-help] Help w/ Chado RPM Build
Brian O'Connor
briandoconnor at gmail.com
Fri Jan 9 15:50:24 EST 2009
Hey Dave, Scott, et al.
I'm trying to update the chado RPMs we're using in the Nelson lab from
version 0.003 to 1.0 of the schema (hopefully these will be ready for
the GMOD meeting too!). So I downloaded the 1.0 schema release and
followed the install readme to build it first by hand before updating
the RPM spec file. Everything worked OK until the ontology load step.
First, two of the URLs referenced in load/tt2/load.conf.tt2 were out of
date. It looks like SourceForge is now using the following URLs:
*
http://obo.cvs.sourceforge.net/viewvc/*checkout*/obo/obo/ontology/OBO_REL/relationship.obo
*
http://obo.cvs.sourceforge.net/viewvc/*checkout*/obo/obo/ontology/anatomy/cell_type/cell.obo
And this doesn't appear to be fixed in cvs HEAD e.g.:
http://gmod.cvs.sourceforge.net/viewvc/*checkout*/gmod/schema/chado/load/tt2/load.conf.tt2
Anyway, that's a minor problem. However when I tried to do a "make
ontologies" step I get the following error:
++++++++++++++++++++++++
...
fetching files for Sequence Ontology
+http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
updated
loading...DBD::Pg::st execute failed: ERROR: null value in column
"cv_id" violates not-null constraint
[for Statement "INSERT INTO cvterm (dbxref_id) VALUES (?)" with
ParamValues: 1='2033'] at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm
line 3314.
DBD::Pg::st execute failed: ERROR: null value in column "cv_id"
violates not-null constraint
[for Statement "INSERT INTO cvterm (dbxref_id) VALUES (?)" with
ParamValues: 1='2033'] at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm
line 3314.
at /usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.pm line 3324
DBIx::DBStag::insertrow('DBIx::DBStag=HASH(0x84ebd40)',
'cvterm', 'HASH(0x8d01e70)', 'cvterm_id') called at
/usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
line 1920
DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
'Data::Stag::StagImpl=ARRAY(0x8d6e3c4)') called at
/usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
line 1333
DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
'Data::Stag::StagImpl=ARRAY(0x8d556f4)', 'HASH(0x8d28fa0)') called at
/usr/lib/perl5/site_perl/
.8.5/DBIx/DBStag.pm line 2077
DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
'Data::Stag::StagImpl=ARRAY(0x8d6b0dc)') called at
/usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
line 1333
DBIx::DBStag::_storenode('DBIx::DBStag=HASH(0x84ebd40)',
'Data::Stag::StagImpl=ARRAY(0x8d1ad5c)') called at
/usr/lib/perl5/site_perl/5.8.5/DBIx/DBStag.p
line 1180
DBIx::DBStag::storenode('DBIx::DBStag=HASH(0x84ebd40)',
'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
/usr/bin/stag-storenode.pl line 88
eval {...} called at /usr/bin/stag-storenode.pl line 87
main::store('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
/usr/bin/stag-storenode.pl line 137
main::__ANON__('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
'Data::Stag::StagImpl=ARRAY(0x8d38e0c)') called at
/usr/lib/perl5/site_perl/5.8.5/Data/Stag/Ba
eHandler.pm line 572
Data::Stag::BaseHandler::end_event('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
'cvterm_relationship') called at /usr/lib/perl5/site_perl/5.8.5/Data/Stag/
aseHandler.pm line 720
Data::Stag::BaseHandler::end_element('Data::Stag::BaseHandler=HASH(0x8bb2cc8)',
'HASH(0x8c810c8)') called at /usr/lib/perl5/vendor_perl/5.8.5/XML/Parser
PerlSAX.pm line 239
XML::Parser::PerlSAX::_handle_end('XML::Parser::PerlSAX=HASH(0x8c46ca0)',
'XML::Parser::Expat=HASH(0x8727b64)', 'cvterm_relationship') called at
/usr/li
/perl5/vendor_perl/5.8.5/XML/Parser/PerlSAX.pm line 79
XML::Parser::PerlSAX::__ANON__('XML::Parser::Expat=HASH(0x8727b64)',
'cvterm_relationship') called at
/usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread
multi/XML/Parser/Expat.pm line 469
XML::Parser::Expat::parse('XML::Parser::Expat=HASH(0x8727b64)',
'FileHandle=GLOB(0x8c7e6e4)') called at
/usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thre
d-multi/XML/Parser.pm line 187
eval {...} called at
/usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi/XML/Parser.pm
line 186
XML::Parser::parse('XML::Parser=HASH(0x87272c4)',
'FileHandle=GLOB(0x8c7e6e4)') called at
/usr/lib/perl5/vendor_perl/5.8.5/XML/Parser/PerlSAX.pm line 14
XML::Parser::PerlSAX::parse('XML::Parser::PerlSAX=HASH(0x8c46ca0)',
'Handler', 'Data::Stag::BaseHandler=HASH(0x8bb2cc8)', 'Source',
'HASH(0x8c1dfa0)') c
lled at /usr/lib/perl5/site_perl/5.8.5/Data/Stag/XMLParser.pm line 69
Data::Stag::XMLParser::parse_fh('Data::Stag::XMLParser=HASH(0x8b31360)',
'FileHandle=GLOB(0x8c7e6e4)') called at
/usr/lib/perl5/site_perl/5.8.5/Data/Sta
/BaseGenerator.pm line 476
Data::Stag::BaseGenerator::parse('Data::Stag::XMLParser=HASH(0x8b31360)',
'-file', 'tmp/song/so.oboxml', '-str', 'undef', '-fh', 'undef') called
at /usr
lib/perl5/site_perl/5.8.5/Data/Stag/XMLParser.pm line 58
Data::Stag::XMLParser::parse('Data::Stag::XMLParser=HASH(0x8b31360)',
'-file', 'tmp/song/so.oboxml', '-str', 'undef', '-fh', 'undef') called
at /usr/lib
perl5/site_perl/5.8.5/Data/Stag/StagImpl.pm line 259
Data::Stag::StagImpl::parse('Data::Stag', '-format', 'undef',
'-file', 'tmp/song/so.oboxml', '-handler',
'Data::Stag::BaseHandler=HASH(0x8bb2cc8)') call
d at /usr/lib/perl5/site_perl/5.8.5/Data/Stag.pm line 179
Data::Stag::AUTOLOAD('Data::Stag', '-format', 'undef', '-file',
'tmp/song/so.oboxml', '-handler',
'Data::Stag::BaseHandler=HASH(0x8bb2cc8)') called at /
sr/bin/stag-storenode.pl line 143
System call 'stag-storenode.pl -d
'dbi:Pg:dbname=chado_v_1.0;host=localhost;port=5432' --user gmod
tmp/song/so.oboxml' failed: 256
Died at /home/gmod/Dev/gmod-1.0/lib/Chado/Builder.pm line 315, <STDIN>
line 1.
make: *** [ontologies] Error 2
++++++++++++++++++++++++
I'm using the following RPMs, see any dependency issues?
httpd-2.0.52-32.ent.centos4
perl-bioperl-1.5-1.9.bp.centos4 (may need > 1.5.2?)
perl-go-perl-0.02-4.bp.centos4
postgresql-server-7.4.17-1.RHEL4.1
ant (missing)
perl-DBI-1.47-1.8.bp.centos4
perl-DBD-Pg-1.49-1.9.bp.centos4
perl-SQL-Translator-0.07-1.4.bp.centos4
perl-Data-Stag-0.08-1.12.bp.centos4
perl-XML-Parser-2.34-5
perl-Module-Build-0.25-1.3.bp.centos4
perl-Class-DBI-0.96-1.4.bp.centos4
perl-Class-DBI-Pg-0.08-1.7.bp.centos4
perl-Class-DBI-Pager-0.06-1.5.bp.centos4
perl-DBIx-DBStag-0.07-1.5.bp.centos4 (manually updated to
DBIx-DBStag-0.10 and dep of DBIx-DBSchema-0.36)
perl-XML-Simple-2.14-1.3.bp.centos4
perl-libwww-perl-5.805-1.12.bp.centos4
perl-Template-Toolkit-2.14-1.9.bp.centos4
perl-Log-Log4perl-0.51-1.5.bp.centos4
Any ideas? Sorry if there's something obvious that I'm doing wrong, I
haven't built a DB from scratch in a long time :-)
Thanks for the help.
--Brian
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