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

[Hilmar Lapp]

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 :
===========================================================