[Gmod-help] Help w/ Chado RPM Build
Scott Cain
scott at scottcain.net
Fri Jan 9 17:29:03 EST 2009
Hi Brian,
Bioperl is almost certainly a problem. Nothing else jumps out at me
at the moment; it's been a while since I've used Pg 7.4, but I don't
think there is a problem there.
Thanks for the info about the ontology links--I wasn't aware that they
were broken.
Scott
On Fri, Jan 9, 2009 at 3:50 PM, Brian O'Connor <briandoconnor at gmail.com> wrote:
> 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 referenced in load/tt2/load.conf.tt2 were out of date.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
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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