[Gmod-help] Help w/ Chado RPM Build
Brian O'Connor
briandoconnor at gmail.com
Fri Jan 16 01:13:59 EST 2009
Hi Scott,
Where you able to debug the ontology loading step? I was able to hack
my way through this but in order to build a proper 1.0 release RPM I
need to get the ontology to load cleanly via the build process.
--Brian
Scott Cain wrote:
> Hi Brian,
>
> I'll look at it tonight; presumably something is broken that needs
> fixing. I'll either get everything fixed or make you a dump.
>
> Scott
>
>
> On Fri, Jan 9, 2009 at 8:08 PM, Brian O'Connor <briandoconnor at gmail.com> wrote:
>> Hey Scott,
>>
>> I updated to BioPerl-1.5.9_2 manually following the directions at
>> bioperl.org and the problem persisted. Any other ideas?
>>
>> I didn't see this on the gmod.org site but do you also distribute db dumps
>> of clean databases (e.g. the default schema and base ontologies loaded)? I
>> could use that to make my RPM.
>>
>> --Brian
>>
>> Scott Cain wrote:
>>> 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 referenced in load/tt2/load.conf.tt2 were out of date.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
>>>>
>>>
>>>
>>
>
>
>
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