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

Fri May 6 17:18:00 UTC 2011

Hey thanks,

I'll give the MacPorts method a go today & let you know how it turns out.  Regards, AJP

From: Jason Stajich <jason.stajich at gmail.com<mailto:jason.stajich at gmail.com>>
Date: Thu, 5 May 2011 18:01:53 -0400
To: Amy Jo Powell <ajpowel at sandia.gov<mailto:ajpowel at sandia.gov>>
Cc: Lincoln Stein <lincoln.stein at gmail.com<mailto:lincoln.stein at gmail.com>>, Christopher Fields <cjfields1 at gmail.com<mailto:cjfields1 at gmail.com>>, 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

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
<https://trac.macports.org/ticket/26468>
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><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><mailto:cjfields1 at gmail.com>>
Cc: Amy Jo Powell <ajpowel at sandia.gov<mailto: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><mailto:bioperl-l at lists.open-bio.org>>, "Supinger, Adam W" <awsupin at sandia.gov<mailto: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><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><mailto:Renata.Musa at oicr.on.ca>>

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