[Gmod-help] Help w/ Chado RPM Build
Scott Cain
scott at scottcain.net
Fri Jan 16 01:47:22 EST 2009
Hi Brian,
I didn't get a chance to work on it--it's been a very busy week. I
just started a test load on code from cvs and it loaded rel and SO
without problem. It's loading GO now, but that will take a while.
I'll give it a try on another computer with gmod 1.0.
Scott
On Fri, Jan 16, 2009 at 1:13 AM, Brian O'Connor <briandoconnor at gmail.com> wrote:
> 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 referenced in load/tt2/load.conf.tt2 were out of date.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
>>>>>
>>>>
>>>>
>>>
>>
>>
>>
>
>
--
------------------------------------------------------------------------
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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