[Bioperl-l] bioperl-1.5.0 RC2

[Fernan Aguero]

+----[ Jason Stajich <jason.stajich at duke.edu> (12.Jan.2005 17:25):
|
| We need people to test on this.  So download, run
|  perl Makefile.PL
|  make
|  make test
| 
| Let us know what breaks. 
|
+----]

This is on FreeBSD-4.10p5 (RELENG_4_10), i386, perl v5.8.5.

A summary of the failed tests follows (anyone knows why I'm
getting percentages over 100%?)

A complete log is available at 
http://genoma.unsam.edu.ar/~fernan/freebsd/bioperl-1.5.0-RC2.tests.gz

And the list of perl modules installed in my box and their
versions is here:
http://genoma.unsam.edu.ar/~fernan/freebsd/p5-ports.txt

If some tests can be fixed just by updating perl modules,
let me know. Perl modules in FreeBSD are installed from the
ports system, so when updating the bioperl port to 1.5 we
should also make sure to update dependencies as needed.
The versions of my installed perl modules are the latest
available in the ports tree (of course there could be newer
versions in CPAN that are not yet in the FreeBSD ports tree)

Fernan


Failed Test           Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/AlignIO.t            255 65280   152  230 151.32%  10-11
39-152
t/AlignUtil.t                       16   14  87.50%  2-15
t/AnnotationAdaptor.t  255 65280    19   36 189.47%  2-19
t/CodonTable.t         255 65280    44    6  13.64%  42-44
t/LocationFactory.t                179    1   0.56%  64
t/OntologyStore.t                    6    1  16.67%  6
t/PAML.t               255 65280   142    0   0.00%  ??
t/PopGen.t             255 65280    85  170 200.00%  1-85
t/ProtPsm.t            255 65280     5    6 120.00%  3-5
t/Registry.t           255 65280    13   11  84.62%  8-13
t/SearchIO.t           255 65280  1216   17   1.40%  170 211 264-265 469 580
                                                     582 584 598 600 643 685-
						     686 713-714 1216
t/SeqFeature.t                     192    2   1.04%  76 81
t/SeqIO.t              255 65280   345  562 162.90%  65-345
t/Species.t            255 65280    21   22 104.76%  11-21
t/StandAloneBlast.t                 18    1   5.56%  3
t/Tree.t               255 65280    26   47 180.77%  3-26
t/TreeBuild.t          255 65280     7   14 200.00%  1-7
t/TreeIO.t             255 65280    50   43  86.00%  28-50
t/Unflattener2.t                    11    2  18.18%  7 10
t/UniGene.t                         63    1   1.59%  12
t/game.t                            23    1   4.35%  9
t/hmmer.t                          136   14  10.29%  8 13 125-136
t/primaryqual.t        255 65280    32    8  25.00%  29-32
t/psm.t                255 65280    48   78 162.50%  10-48
t/qual.t               255 65280    12    0   0.00%  ??
t/simpleGOparser.t                 101    5   4.95%  78-79 83-84 87
t/singlet.t                          3    2  66.67%  2-3
114 subtests skipped.
Failed 27/193 test scripts, 86.01% okay. 680/8956 subtests failed, 92.41% okay.