[Bioperl-l] ps-another attempt at installing Ace for BioPerl
Powell Phd, Amy Jo
ajpowel at sandia.gov
Thu May 5 17:38:27 UTC 2011
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>
>
>
More information about the Bioperl-l
mailing list