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

Dave Howorth dhoworth at mrc-lmb.cam.ac.uk
Wed Apr 21 12:22:12 EDT 2004

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'."

Cheers, Dave
Dave Howorth
MRC Centre for Protein Engineering
Hills Road, Cambridge, CB2 2QH
01223 252960

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