[BioSQL-l] Help installing BioSQL and its (Perl) dependencies

Hilmar Lapp hlapp at drycafe.net
Wed Jan 13 12:04:48 EST 2010 

(hit send erroneously ...)

Hi Sammy,

please always direct your questions to the mailing list. There are  
many more people there who can help you out.

Have you looked at the INSTALL file that comes with BioSQL and tried  
to follow the instructions therein? If yes, what did you find not to  
work?

	-hilmar

On Jan 13, 2010, at 11:22 AM, Bolin, Samuel wrote:

> Mark and Hilmar
>
> I am working with Amy Powell on getting BioSQL up and running
> Decided to take a different tact and am now using Fedora
> Was able to get MySQL BioPerl installed along with getting past the  
> DBD and DBI issues
> However I have read thru the documentation and have been unable to  
> figure out how BioSQL ties in must less get it installed
> Any guidance?
>
> Sammy
>
> From: Powell Phd, Amy Jo
> Sent: Thursday, January 07, 2010 10:29 AM
> To: Mark A. Jensen; Hilmar Lapp
> Cc: biosql-l; Bolin, Samuel
> Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl)  
> dependencies
>
> Hi there-
>
> Thanks very much for your suggestion.  We’ll give it a try and see  
> what happens.  Sincerely, AJP
>
>
> On 1/7/10 9:08 AM, "Mark A. Jensen" <maj at fortinbras.us> wrote:
>
> This portion
>
> > Running install for module 'DBD::mysql'
> > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz
> >  Has already been unwrapped into directory
> > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL
> >  Has already been made
> > Running make test
> > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> > t/00base.t .................. 1/6
> > #   Failed test 'use DBD::mysql;'
> > #   at t/00base.t line 21.
> > #     Tried to use 'DBD::mysql'.
> > #     Error:  Can't load
>
> suggests that, though DBD::mysql was made, the module can't be
> found by perl (is not in @INC). You could try installing from scratch
> again
>
> cpan> fforce install DBD::mysql
>
> The other issue may be that your mysql installation can't be found  
> or encounters
> an error when
> DBD::mysql is loaded. Try at the command line
>
> $ perl -MDBD::mysql -e 1
>
> and see if any more helpful errors ensue.
>
> MAJ
>
> ----- Original Message -----
> From: "Hilmar Lapp" <hlapp at drycafe.net>
> To: "Powell Phd, Amy Jo" <ajpowel at sandia.gov>
> Cc: "biosql-l" <biosql-l at lists.open-bio.org>; "Bolin,Samuel"
> <sabolin at sandia.gov>
> Sent: Thursday, January 07, 2010 10:49 AM
> Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl)  
> dependencies
>
>
> > Hi Amy,
> >
> > this looks like a problem with installing DBD::mysql, not BioSQL.  
> I  don't
> > know how you built DBD::mysql and DBI, and I haven't encountered   
> this error
> > (but maybe someone else on the BioSQL list has come across   
> this?), so your
> > best avenue for getting help is probably the  DBD::mysql mailing  
> list.
> >
> > Cheers,
> >
> > -hilmar
> >
> > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote:
> >
> >> Dear Hilmar,
> >>
> >> Happy New Year!  I hope you had enjoyable holidays.  So, my sys  
> admin
> >> colleague and I are trying to get BioSQL (with a BioPerl  
> language  binding)
> >> up and running ASAP.
> >>
> >> We have successfully installed MySQL and BioPerl.  We are having   
> trouble,
> >> however, getting the DBD::mysql module installed (on a Macbook  
> Pro  running
> >> OS X 10.6.1) to finish the last steps of BioSQL installation.   
> The  error
> >> message for our attempt is pasted below.  We have also attempted  
> a  manual
> >> install, and get the same result (i.e., croaking at the make test
> >> step)-failed installation.
> >>
> >> Would you please guide us through the necessary final steps in  
> getting
> >> BioSQL up and running?  Any help you can provide would be greatly
> >> appreciated.  Thanks very much and I look forward to hearing from  
> you.
> >> Sincerely, AJP
> >>
> >>
> >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION]
> >>
> >> cpan[1]> install Bundle::DBD::mysql
> >> CPAN: Storable loaded ok (v2.21)
> >> Going to read '/var/root/.cpan/Metadata'
> >>  Database was generated on Wed, 06 Jan 2010 09:01:01 GMT
> >> CPAN: YAML loaded ok (v0.70)
> >> Going to read 52 yaml files from /var/root/.cpan/build/
> >> CPAN: Time::HiRes loaded ok (v1.9711)
> >> DONE
> >> Restored the state of none (in 1.1851 secs)
> >>  Has already been unwrapped into directory
> >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL
> >> DBI is up to date (1.609).
> >> Running install for module 'DBD::mysql'
> >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz
> >>  Has already been unwrapped into directory
> >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL
> >>  Has already been made
> >> Running make test
> >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> >> t/00base.t .................. 1/6
> >> #   Failed test 'use DBD::mysql;'
> >> #   at t/00base.t line 21.
> >> #     Tried to use 'DBD::mysql'.
> >> #     Error:  Can't load
> >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ 
> auto/ DBD/mys
> >> ql/mysql.bundle' for module DBD::mysql:
> >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/  
> arch/auto/D
> >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix
> >> #   Referenced from:
> >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ 
> auto/ DBD/mysq
> >> l/mysql.bundle
> >> #   Expected in: flat namespace
> >> #  in
> >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ 
> auto/ DBD/mysq
> >> l/mysql.bundle at
> >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ 
> DynaLoader.pm  line
> >> 207.
> >> #  at (eval 7) line 2
> >> # Compilation failed in require at (eval 7) line 2.
> >> # BEGIN failed--compilation aborted at (eval 7) line 2.
> >> Bailout called.  Further testing stopped:  Unable to load  
> DBD::mysql
> >> FAILED--Further testing stopped: Unable to load DBD::mysql
> >> make: *** [test_dynamic] Error 255
> >>  CAPTTOFU/DBD-mysql-4.013.tar.gz
> >>  make test -- NOT OK
> >> //hint// to see the cpan-testers results for installing this  
> module,  try:
> >>  reports CAPTTOFU/DBD-mysql-4.013.tar.gz
> >> Running make install
> >>  make test had returned bad status, won't install without force
> >> Failed during this command:
> >> CAPTTOFU/DBD-mysql-4.013.tar.gz              : make_test NO
> >>
> >>
> >
> > --
> > ===========================================================
> > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> > ===========================================================
> >
> >
> >
> >
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biosql-l
> >
> >
>
>
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
===========================================================

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