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

Jason Stajich jason at cgt.duhs.duke.edu
Wed Apr 21 12:35:59 EDT 2004

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

> Cheers, Dave

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

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