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

[Chris Fields]

Amy,

Are you installing this using the system perl (which I think is perl 5.10.1)?  I'm running BioPerl on the same OS w/o problems, but I am also using a bit more of a custom setup (perlbrew in particular, which allows me to switch perl versions, and cpanminus).  In general I have found the UNIX install instructions to work fine.

Having a more detailed list of problems you have encountered would help tremendously as well.  Specifically, how exactly are you installing BioPerl?  What tests are failing?

Also, by distributions, do you mean something like fink or macports?  I think a bioperl version exists on macports, but I'm not sure how up-to-date it is.

chris

On May 5, 2011, at 11:20 AM, 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>
> Date: Thu, 5 May 2011 09:46:08 -0400
> To: Christopher Fields <cjfields1 at gmail.com>
> Cc: Amy Jo Powell <ajpowel at sandia.gov>, BioPerl List <bioperl-l at lists.open-bio.org>, "Supinger, Adam W" <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> 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>