[Bioperl-l] Makefile.PL and cvs.bioperl.org

Chris Dagdigian dag at sonsorol.org
Wed Apr 21 14:41:42 EDT 2004

I just uploaded a new Bundle::BioPerl to CPAN -- should be available 
within a few hours on search.cpan.org. Not sure how long it will take to 
filter out to all the CPAN mirrors, probably 24 hours or so.

The new Bundle has "SVG::Graph" as an additional dependency.

That module in turn depends on:

SVG is in the Bundle::BioPerl but I left the others out. The CPAN script 
will follow the SVG::Graph dependency tree if the user allows


> The uploaded file
>     Bundle-BioPerl-2.1.5.tar.gz
> has entered CPAN as
>   file: $CPAN/authors/id/C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz
>   size: 3175 bytes
>    md5: fb3a5f1873b7c91f699de204aaad0277
> No action is required on your part
> Request entered by: CRAFFI (Chris Dagdigian)
> Request entered on: Wed, 21 Apr 2004 18:29:55 GMT
> Request completed:  Wed, 21 Apr 2004 18:30:24 GMT

Jason Stajich wrote:

> On Wed, 21 Apr 2004, Dave Howorth wrote:
>>Based on my experience, I'd like to suggest the following changes to
>>make it easier for neophytes to patch a bioperl release:
>>On http://cvs.bioperl.org
>>At the bottom of the page, add an example on how to patch an existing
>>installation. Or refer to somewhere else that does. Specifically give an
>>example of the use of tags and explain where to find the upgrade/install
>>instructions (I previously installed bioperl from CPAN so I had no idea
>>how to use the cvs system. The page asks "Do you really want to be
>>here?" to which my answer is "No, but I have to be because of bugs", and
>>I think the page should address that audience). e.g.:
>>   "To patch an existing release, find the cvs tag of the appropriate
>>    branch (need to describe how!!) then type:
>>      cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/bioperl \
>>      checkout -r branch-1-4 bioperl-live
>>    Then follow the normal install instructions in the INSTALL document
>>in the top level directory (probably need more here!!!)"
>>In Makefile.PL
>>It picked up a missing dependency on GD::SVG and on SVG, but it failed
>>to pick up on a dependency on SVG::Graph.
>>I'd also suggest that where Makefile.PL prints out:
>>     "Enjoy the rest of bioperl, which you can use after going
>>     'make install'"
>>it could increase the warm fuzziness if it was expanded to say:
>>     "You can install the external packages now and then rerun
>>     'make Makefile.PL' or just enjoy the rest of bioperl,
>>     which you can use after going 'make install'."
> Allen needs to add this to Makefile.PL and Chris needs to add it to
> Bundle::BioPerl.
>>Cheers, Dave

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