[MOBY-dev] Fwd: Re: [MOBY-l] error when do make test

[Mark Wilkinson]

Hmmmm.... that's a tricky one.  DBD::mysql should not be required if the  
person is running MOBY as a client only, but it is required when running  
it as a Registry.  I don't think that MOBY::OntologyServer is used  
client-side either.  AFAIK MOBY::Client::OntologyServer is used by the  
client software.

The upshot is that people not running a registry do not need to  
successfully load the MOBY::Central module, or the MOBY::OntologyServer  
module, so the first test (Central.t) should not be run for these cases.   
Thus, DBD::mysql is also not a requirement in these cases.

M



On Wed, 15 Feb 2006 12:37:04 -0800, Frank Gibbons  
<francis_gibbons at hms.harvard.edu> wrote:

> Mark,
>
> it looks like DBD::mysql is now required (see Nicholas's email below),  
> because of MOBY::OntologyServer.pm, is that right? I see that the  
> constructor new() tries to instantiate a connection to a remote DB. If  
> it's a requirement, then I'll put it into the Makefile.PL, otherwise  
> perhaps there's a way we could find a work-around for users who don't  
> have it installed.
>
> -Frank
>
> At 02:13 PM 2/15/2006, you wrote:
>> Hello,
>>
>> I just downloaded the biomoby tarball from the CVS reprository
>> (http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=biomoby),  
>> and
>> tried to install it here to my system.
>>
>> So I went to moby/moby-live/Perl folder, and do "perl Makefile.PL
>> PREFIX=/MyInstallationFolder".
>> Then, I do make.
>>
>> But it seems that it's failing when i did the make test.
>> I copied and pasted the error message in the bottom of this email.
>>
>> Do you guys can give me any clue why this happen? Maybe I miss  
>> something?
>>
>> I did the same thing with the latest code release version  
>> (09/16/2004).., but it
>> seems I can install it without this problem.
>>
>>
>> Thanks a lot,
>> Nicholas.
>>
>>
>> alhagib 86 % make test
>> PERL_DL_NONLAZY=1 /p/perl/bin/perl "-MExtUtils::Command::MM" "-e"
>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>> t/Central...................................#     Failed test  
>> (t/Central.t at
>> line 26)
>> #     Tried to use 'MOBY::Central'.
>> t/Central...................................NOK 1#     Error:  Can't  
>> locate
>> DBD/mysql.pm in @INC (@INC contains:
>> /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib
>> /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/arch
>> /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi
>> /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4/sun4-solaris-thread-multi
>> /.ulphius/p29/www-cgi/cgi-bin/nsutanto/perl/lib/site_perl/5.8.4
>> /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi
>> /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi  
>> /p/perl-5.8.4/lib/5.8.4
>> /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi
>> /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi
>> /p/perl-5.8.4/lib/site_perl/5.8.4
>> /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi
>> /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .
>> /p/perl-5.8.4/lib/5.8.4/sun4-solaris-thread-multi  
>> /p/perl-5.8.4/lib/5.8.4
>> /p/perl-5.8.4/lib/site_perl/5.8.4/sun4-solaris-thread-multi
>> /p/perl-5.8.4/lib/site_perl/5.8.4 /p/perl-5.8.4/lib/site_perl .) at
>> /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/OntologyServer.pm
>> line 70.
>> # BEGIN failed--compilation aborted at
>> /.ulphius/p29/www-cgi/cgi-bin/nsutanto/moby/moby-live/Perl/blib/lib/MOBY/OntologyServer.pm
>> line 70.
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115,  
> USA.
> Tel: 617-432-3555       Fax: 617-432-3557        
> http://llama.med.harvard.edu/~fgibbons
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115,  
> USA.
> Tel: 617-432-3555       Fax: 617-432-3557        
> http://llama.med.harvard.edu/~fgibbons



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital