[Bioperl-l] Bio::DB::GFF

[Lincoln Stein]

It sounds like Perl's dbd::mysql driver has to be reinstalled because the 
libmysql library changed.

If you don't use the mysql adaptor for Bio::DB::GFF, simply rerun Bioperl's 
Makefile.PL  and answer "no" when it asks you if you want to run the 
Bio::DB::GFF tests (it will run using the in-memory adaptor).

Lincoln

On Wednesday 16 July 2003 04:49 pm, Eley Greg wrote:
> I recently upgraded my system to RedHat 9 and reinstalled Bioperl.  All
> is well except for database access.  When I run the Bio::DB::GFF tests,
> they all fail with the following error:
>
> t/BioDBGFF...................install_driver(mysql) failed: Can't load
> '/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/my
>sql.so' for module DBD::mysql:
> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi/auto/DBD/mysql/mys
>ql.so: undefined symbol: mysql_ssl_set at
> /usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229, <T>
> line 6.
>  at (eval 11) line 3
> Compilation failed in require at (eval 11) line 3, <T> line 6.
> Perhaps a required shared library or dll isn't installed where expected
>  at blib/lib/Bio/DB/GFF/Adaptor/dbi/caching_handle.pm line 140
> t/BioDBGFF...................FAILED tests 1-116
>         Failed 116/116 tests, 0.00% okay
>
> The mysql_ssl_set is a flag that can be set if mysql_ssl flag is set to
> on.  However, I have no idea how to change this or if there is an ssl
> module that I installed that is causing the problem.  Any help is
> appreciated.
>
> Thank you.
>
> Greg Eley
>
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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