[Bioperl-l] Re: go-perl

[Hilmar Lapp]

You should probably upgrade to a snapshot from the CVS main trunk (in  
essence equivalent to a 1.5.x version) if you want to use Bioperl.

As ChrisM said, for go-perl bioperl is not required. In fact, the next  
version of Bioperl will optionally depend on go-perl if you want .obo  
formats supported.

	-hilmar

On Jul 1, 2005, at 3:51 AM, dsam at ucsd.edu wrote:

> Hello,
>
> I tried to install BioPerl using CPAN, but I get quite a few failed  
> tests.
>
> I need BioPerl in order to install the GO Perl API.
> These are needed to calculate semantic similarity based on Gene
> Ontology (http://www.cs.man.ac.uk/~phillord/semantic_sim.html).
>
> I was wondering what does each failed test mean (e.g. simpleGOparser)
> and if the failed tests can be ignored.
> Any insight would be greatly appreciated.
>
> Below are the failed tests:
>
> Thanks,
> Daniel
>
> /**************
> CPAN
> **************/
>
> cpan> d /bioperl/
> Distribution    A/AL/ALLENDAY/bioperl-microarray-0.1.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-0.05.1.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-0.6.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-0.7.0.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.0.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.0.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.2.1.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.2.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.2.3.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-1.4.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-db-0.1.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-gui-0.7.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-run-1.2.2.tar.gz
> Distribution    B/BI/BIRNEY/bioperl-run-1.4.tar.gz
> Distribution    B/BO/BOZO/Fry-Lib-BioPerl-0.15.tar.gz
> Distribution    C/CR/CRAFFI/Bundle-BioPerl-2.1.5.tar.gz
> 18 items found
>
> cpan>install B/BI/BIRNEY/bioperl-1.4.tar.gz
> ...
> ...
>> </seqDiff>
> t/Variation_IO...............FAILED tests 15, 20, 25
>         Failed 3/25 tests, 88.00% okay
> t/WABA.......................ok
> t/XEMBL_DB...................ok
> Failed Test        Stat Wstat Total Fail  Failed  List of Failed
> ----------------------------------------------------------------------- 
> --------
> t/BioFetch_DB.t                  27    2   7.41%  20-21
> t/DB.t                           78    2   2.56%  30-31
> t/EMBL_DB.t                      15    2  13.33%  13-14
> t/Ontology.t        255 65280    50  100 200.00%  1-50
> t/TreeIO.t                       41    1   2.44%  42
> t/Variation_IO.t                 25    3  12.00%  15 20 25
> t/simpleGOparser.t  255 65280    98  196 200.00%  1-98
> 121 subtests skipped.
> Failed 7/179 test scripts, 96.09% okay. 156/8268 subtests failed,  
> 98.11%
> okay.
> make: *** [test_dynamic] Error 2
>   /usr/bin/make test -- NOT OK
> Running make install
>   make test had returned bad status, won't install without force
>
> cpan>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------