[Gmod-help] install Bundle::GMOD failed

[Scott Cain]

Hi Fred,

Two things:

* You don't need DBD::mysql.  The Bundle::GMOD that is on CPAN is very
old; I attempted to update it, but only realized I failed when I got
your email.  I'm now trying again.

* If you decide you do want DBD::mysql for GBrowse, it is generally
easier to get DBD modules to install by hand, as most people run cpan
as root, but the root user generally doesn't have appropriate
permissions to create databases, so the tests fail.

Scott


On Fri, Nov 7, 2008 at 12:39 PM, Peng, Fred <fredyfpeng at ualberta.ca> wrote:
> Hello,
>
> I am trying to install Chado for a large-scale genomics project. To install
> prerequisites (using CPAN), everything looks good until installing
> Bundle::GMOD. I got the following error message:
>
> Is it OK to try to connect to the Internet? [yes]
> Fetching with LWP:
>   http://www.perl.org/CPAN/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.010.tar.gz
> Use of uninitialized value in concatenation (.) or string at
> /usr/lib/perl5/5.8.8/i386-linux-thread-multi/Scalar/Util.pm line 30, <STDIN>
> line 2.
> Fetching with LWP:
>   http://www.perl.org/CPAN/authors/id/C/CA/CAPTTOFU/CHECKSUMS
> Catching error: "Undefined subroutine &Compress::Zlib::gzopen called at
> /usr/lib/perl5/5.8.8/CPAN/Tarzip.pm line 122.\cJ" at
> /usr/lib/perl5/5.8.8/CPAN.pm line 359
>         CPAN::shell() called at /usr/bin/cpan line 198
>
> This looks like a CPAN issue, however CPAN was perfectly fine while
> installing BioPerl and GO-Perl. Can you please pass this message to a Chado
> expert to figure out what goes wrong here? I desperately need some help
> after many attempts.
>
> Many thanks in advance.
>
> Fred
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research