perl error in using DBD::mysql

Aghori · 07-30-2013, 07:29 AM

Hello all , i amworking on orthomcl software which requirs mysql , when i give the command
[cdac@nbri bin]$ orthomclLoadBlast my_orthomcl/orthomcl.configmy_orthomcl/similarSequence.txt

it gives

Can't load '/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so' for module DBD::mysql: libmysqlclient.so.15: cannot open shared object file: No such file or directory at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230, <F> line 5.
at /storage/home/cdac/OrthoMCL/orthomclSoftware-v2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 48
Compilation failed in require at /storage/home/cdac/OrthoMCL/orthomclSoftware-v2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 48, <F> line 5.

mysql.so file is present then why it is giving this error??and how to solve this ?

daniel w. · 07-30-2013, 07:42 AM

Does perl exists in Your system?

Which distro do You use?

perl -v paste it here

regards

Aghori · 07-30-2013, 07:46 AM

[cdac@nbri ~]$ perl -v

This is perl, v5.8.8 built for x86_64-linux-thread-multi

Copyright 1987-2006, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to the
Internet, point your browser at http://www.perl.org/, the Perl Home Page.

daniel w. · 07-30-2013, 07:54 AM

What disibution are u using?

Meybe there are missing perl-mysql modules in your system?

Thats a shot, im not an expert. And in addition my english isnt that good.
Sorry then.

regards
D.W

pan64 · 07-30-2013, 08:07 AM

does this file exist? '/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so'. Yes, you may need to install a few perl modules

TB0ne · 07-30-2013, 08:10 AM

Quote:

Originally Posted by Aghori

Hello all , i amworking on orthomcl software which requirs mysql , when i give the command
[cdac@nbri bin]$ orthomclLoadBlast my_orthomcl/orthomcl.configmy_orthomcl/similarSequence.txt
it gives

Code:

Can't load '/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so' for module DBD::mysql: libmysqlclient.so.15: cannot open shared object file: No such file or directory at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/DynaLoader.pm line 230, <F> line 5.
 at /storage/home/cdac/OrthoMCL/orthomclSoftware-v2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 48
Compilation failed in require at /storage/home/cdac/OrthoMCL/orthomclSoftware-v2.0.8/bin/../lib/perl/OrthoMCLEngine/Main/Base.pm line 48, <F> line 5.

mysql.so file is present then why it is giving this error??and how to solve this ?

There may be a mysql.so file, but is it for Perl, and is it in the path referenced above?

Go to CPAN.org, download the package and install it:
http://search.cpan.org/~capttofu/DBD-mysql-4.023/

Aghori · 07-30-2013, 08:13 AM

yes.. /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so file is there but it is unable to load @ pan64

pan64 · 07-30-2013, 08:19 AM

file '/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so'

Aghori · 07-30-2013, 08:38 AM

which modules i need to install in my machine to run it properly ?? (mysql is already installed)

TB0ne · 07-30-2013, 10:41 AM

Quote:

Originally Posted by Aghori

which modules i need to install in my machine to run it properly ?? (mysql is already installed)

I posted a link to the missing perl module above. Did you not see it? There is a DOWNLOAD link on it...click it, save it to your system, and follow the installation instructions. Typically:

perl Makefile.PL
make
make test
make install

That's it. If it complains about any missing prerequisites, then download them and install them first. Simple.