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

Thu May 5 19:14:53 UTC 2011

Hi Chris,

OOOOOOOH PHOOOOOEY...

I already closed that CPAN window :  (

I can regenerate the error, tho', if you would like?

On 5/5/11 1:12 PM, "Chris Fields" <cjfields at illinois.edu> wrote:

>Amy,
>
>I need that (...) part you excised, I'm assuming it contains the actual
>test failures (the rest is the summary of the overall test fails but
>doesn't indicate *why* they failed).  You can attach it if needed, or
>register and file a bug report and add it there (probably the best way,
>so we don't lose track of this):
>
>https://redmine.open-bio.org/projects/bioperl
>
>I can do that if you don't have time.
>
>chris
>
>PS - Just so you don't lose faith in case I don't get back to you, I will
>be tied up with setting up a symposium the rest of today and all day
>tomorrow.
>
>On May 5, 2011, at 1:46 PM, Powell Phd, Amy Jo wrote:
>
>> 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>
>>> 
>>> 
>> 
>> 
>> 
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>> Bioperl-l at lists.open-bio.org
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>
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