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

[Chris Fields]

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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