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

Thu May 5 18:31:54 UTC 2011

Or even 'install Bio::Perl' should work, if the CPAN index is up-to-date (it should install the latest).

chris

On May 5, 2011, at 1:04 PM, Kevin Brown wrote:

> I notice that CPAN is returning quite a few different bundles.
> 
> Try "install CJFIELDS/BioPerl-1.6.900.tar.gz" and see what that gives
> you.
> 
> Kevin Brown
> Center for Innovations in Medicine
> Biodesign Institute
> Arizona State University 
> 
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Powell Phd, Amy Jo
>> Sent: Thursday, May 05, 2011 10:38 AM
>> To: Chris Fields
>> Cc: Lincoln Stein; BioPerl List; Supinger,Adam W
>> Subject: Re: [Bioperl-l] ps-another attempt at installing Ace for
>> BioPerl
>> 
>> Hi Chris,
>> 
>> I've (repeatedly) tried to install (all relevant possible versions)
>> using
>> by sudo'ing a cpan window.  Here is the version of perl on my machine:
>> 
>> s930712:go_daily-termdb-tables ajpowel$ perl -v
>> 
>> This is perl, v5.10.0 built for darwin-thread-multi-2level
>> (with 2 registered patches, see perl -V for more detail)
>> 
>> 
>> Here are the errors that are typically generated (in my attempts to
>> install):
>> 
>> 
>> cpan[7]> i /BioPerl/
>> 
>> Bundle    Bundle::BioPerl        (CRAFFI/Bundle-BioPerl-2.1.8.tar.gz)
>> Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
>> Distribution    CJFIELDS/BioPerl-1.6.1.tar.gz
>> Distribution    CJFIELDS/BioPerl-1.6.900.tar.gz
>> Distribution    CJFIELDS/BioPerl-Run-1.006900.tar.gz
>> Distribution    CRAFFI/Bundle-BioPerl-2.1.8.tar.gz
>> Module  < Bio::LiveSeq::IO::BioPerl (CJFIELDS/BioPerl-1.6.1.tar.gz)
>> Module  < Fry::Lib::BioPerl      (BOZO/Fry-Lib-BioPerl-0.15.tar.gz)
>> Author          BIOPERLML ("Bioperl-l" <bioperl-l at lists.open-bio.org>)
>> 9 items found
>> 
>> install Bundle::BioPerl
>> 
>> 
>> Test Summary Report
>> -------------------
>> t/testindexer.t (Wstat: 768 Tests: 5 Failed: 3)
>>  Failed tests:  2-3, 5
>>  Non-zero exit status: 3
>>  Parse errors: Bad plan.  You planned 11 tests but ran 5.
>> Files=2, Tests=15,  0 wallclock secs ( 0.02 usr  0.01 sys +  0.06 cusr
>> 0.01 csys =  0.10 CPU)
>> Result: FAIL
>> Failed 1/2 test programs. 3/15 subtests failed.
>> make: *** [test_dynamic] Error 255
>>  MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz
>> one dependency not OK (Bio::Index::AbstractSeq); additionally test
>> harness
>> failed
>>  /usr/bin/make test -- NOT OK
>> //hint// to see the cpan-testers results for installing this module,
>> try:
>>  reports MINGYILIU/Bio-ASN1-EntrezGene-1.10-
>> withoutworldwriteables.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
>> TWH/GD-SVG-0.33.tar.gz                       : make_test NO one
>> dependency not OK (GD); additionally test harness failed
>> MINGYILIU/Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz:
>> make_test NO one dependency not OK (Bio::Index::AbstractSeq);
>> additionally
>> test harness failed
>> CJFIELDS/BioPerl-1.6.1.tar.gz                : make_test NO 2
>> dependencies missing (Ace,GraphViz)
>> 
>> 
>> 
>> Bottom line, the whole installation appears to fail (no matter what
>> package try to install) b/c of dependency issues (I.e., GraphViz &
>> Ace).
>> My colleague has run into the same problems.
>> 
>> Sorry, I maybe used the wrong jargon when I said 'distribution.'  I
>> always
>> use CPAN when installing perl modules.  Make sense?   Any
> guidance/help
>> you could offer would be greatly appreciated.  Regards, AJP
>> 
>> 
>> 
>> 
>> 
>> 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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