[Bioperl-l] Re: go-perl

[dsam at ucsd.edu]

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>