[Bioperl-l] ps-another attempt at installing Ace for BioPerl

[Jason Stajich]

macports works pretty well now - I have submitted some additional packages so that it will be as easy as running this - which i was able to install on a clean machine.

$ port install bioperl

I'm not sure they accepted my bioperl one yet though - but it is attached as #3 portfile on that page or in my github below. I think I got some of the syntax not quite right, but it definitely worked when it comes to doing the installation.
 https://trac.macports.org/ticket/26468

My ports are here but I've submitted them to macports so they'll be part of the master repo:
https://github.com/hyphaltip/macports

-jason

On May 5, 2011, at 12:20 PM, Powell Phd, Amy Jo wrote:

> Hi Chris & Lincoln,
> 
> A fully installable & useable package/bundle/distribution of BioPerl for the (large) community of Mac users would be greatly appreciated.
> 
> My colleagues and I, all Mac users, have not been able to load BioPerl successfully onto our machines.
> 
> Here are the specs for my particular machine:  MacBook Pro running SnowLeopardOSX (Mac OS X 10.6.7 (10J869)).
> 
> Detailed instructions on how to install a new version would also be greatly appreciated.  Thanks very much.  Regards, AJP
> 
> 
> 
> From: Lincoln Stein <lincoln.stein at gmail.com<mailto:lincoln.stein at gmail.com>>
> Date: Thu, 5 May 2011 09:46:08 -0400
> To: Christopher Fields <cjfields1 at gmail.com<mailto:cjfields1 at gmail.com>>
> Cc: Amy Jo Powell <ajpowel at sandia.gov<mailto:ajpowel at sandia.gov>>, BioPerl List <bioperl-l at lists.open-bio.org<mailto:bioperl-l at lists.open-bio.org>>, "Supinger, Adam W" <awsupin at sandia.gov<mailto:awsupin at sandia.gov>>
> Subject: Re: [Bioperl-l] ps-another attempt at installing Ace for BioPerl
> 
> I think we should remove Ace from bioperl; there can't be that many people still using it, and I'm not devoting any cycles to maintaining the package. I'm happy to do the dirty deed unless there's a strong objection.
> 
> Lincoln
> 
> On Wed, May 4, 2011 at 8:50 PM, Christopher Fields <cjfields1 at gmail.com<mailto:cjfields1 at gmail.com>> wrote:
> (cc'ing the main bioperl list)
> 
> Amy,
> 
> For future correspondence you should contact the bioperl mailing list.  You can subscribe to it here if needed:
> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> As for the modules in question (AcePerl and GraphViz), these aren't absolutely required for most BioPerl functionality; tests that required them are designed to skip if the modules aren't present.  Have you tried *not* installing those and running tests?
> 
> chris
> 
> On May 4, 2011, at 6:08 PM, Powell Phd, Amy Jo wrote:
> 
>> Hi there,
>> 
>> FY:  I made another attempt at installing an Ace package that BioPerl can (hopefully) use, to no avail:
>> 
>> 
>> LDS/AcePerl-1.92.tar.gz
>> /usr/bin/make test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module, try:
>> reports LDS/AcePerl-1.92.tar.gz
>> Running make install
>> make test had returned bad status, won't install without force
>> Failed during this command:
>> LDS/AcePerl-1.92.tar.gz                      : make_test NO
>> 
> 
> 
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> 
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa at oicr.on.ca<mailto:Renata.Musa at oicr.on.ca>>
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