[Bioperl-l] Installing Bioperl - Dependencies problem

[Jason Stajich]

On Thu, 14 Aug 2003, Anelda Boardman wrote:

> Hallo,
>
> I've been trying to install Bioperl, but ran into some trouble with the
> dependencies...  After running 'perl Makefile.PL' I got the message that
> Ace and DBD::mysql are needed.
>
You nnly need these if you want to run Bio::DB::GFF (DBD::mysql) and
Bio::SeqIO::ace (Ace)

> I downloaded DBD::mysql-2.9002 from CPAN and tried to install it according
> to the instructions. 'perl Makefile.PL' runs smoothly, but when I want to
> 'make', something goes wrong and I can't figure out what to do to solve
> the problem. Please could someone help me?
>
> This is part of the error message:
>

DBD::mysql requires you have installed the mysql libraries on your system
- if you are using a linux distro - something like mysql and mysql-devel
are needed.
But you only have to do this if you want to use modules which need
DBD::mysql (Bio::DB::GFF with a mysql backend).

> [root at jive DBD-mysql-2.1028]# make
> cp lib/DBD/mysql.pm blib/lib/DBD/mysql.pm
> cp lib/DBD/mysql/INSTALL.pod blib/lib/DBD/mysql/INSTALL.pod
> cp lib/Mysql.pm blib/lib/Mysql.pm
> cp lib/Mysql/Statement.pm blib/lib/Mysql/Statement.pm
> cp lib/DBD/mysql.pod blib/lib/DBD/mysql.pod
> cp lib/Bundle/DBD/mysql.pm blib/lib/Bundle/DBD/mysql.pm
> cc -c  -I/usr/local/lib/perl5/site_perl/5.8.0/i686-linux/auto/DBI
> -I'/usr/include' -fno-strict-aliasing -D_LARGEFILE_SOURCE
> -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O3   -DVERSION=\"2.1028\"
> -DXS_VERSION=\"2.1028\" -fpic
> "-I/usr/local/lib/perl5/5.8.0/i686-linux/CORE"   dbdimp.c
> In file included from dbdimp.c:29:
> dbdimp.h:31:49: mysql.h: No such file or directory
> dbdimp.h:32:49: errmsg.h: No such file or directory
> In file included from dbdimp.c:29:
> dbdimp.h:116: parse error before "MYSQL"
> dbdimp.h:116: warning: no semicolon at end of struct or union
> dbdimp.h:122: parse error before '}' token
> dbdimp.h:151: parse error before "MYSQL_RES"
> dbdimp.h:151: warning: no semicolon at end of struct or union
> dbdimp.h:164: parse error before '}' token
> In file included from dbdimp.c:29:
>
>
> What should I do?
>
> Thanks!
> Anelda
>
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu