[Gmod-help] Help w/ Chado RPM Build
Scott Cain
scott at scottcain.net
Fri Jan 9 21:12:57 EST 2009
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 referenced in load/tt2/load.conf.tt2 were out of date.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
>>>
>>
>>
>>
>
>
--
------------------------------------------------------------------------
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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