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

[Powell Phd, Amy Jo]

PS-

More errors obtained in trying to install base bioperl progs:

cpan[3]> install Bio::Root::Build

(...)

Result: FAIL
Failed 21/348 test programs. 38273/59614 subtests failed.
  CJFIELDS/BioPerl-1.6.900.tar.gz
  ./Build test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
  reports CJFIELDS/BioPerl-1.6.900.tar.gz
Running Build install
  make test had returned bad status, won't install without force
Failed during this command:
 CJFIELDS/BioPerl-1.6.900.tar.gz              : make_test NO





On 5/5/11 10:45 AM, "Chris Fields" <cjfields at illinois.edu> wrote:

>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
>>>> >
>>>> 
>>>> 
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>> 
>>> 
>>> 
>>> -- 
>>> 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>
>
>