[Bioperl-l] ps-another attempt at installing Ace for BioPerl
Kevin Brown
Kevin.M.Brown at asu.edu
Thu May 5 18:04:11 UTC 2011
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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