[Bioperl-l] bioperl-1.5.0 RC2

[Tim Erwin]

I am using Fedora Core 3 with perl, v5.8.5 built for i386-linux-thread-
multi. 


make test output:



t/DBCUTG.....................ok
        22/24 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/DBFasta....................ok
t/DNAMutation................ok
t/Domcut.....................ok
        22/25 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/ECnumber...................ok
t/ELM........................ok 9/14
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
500 (Internal Server Error) Can't connect to elm.eu.org:80 (connect:
timeout)
Content-Type: text/plain
Client-Date: Fri, 14 Jan 2005 01:29:27 GMT
Client-Warning: Internal response

500 Can't connect to elm.eu.org:80 (connect: timeout)

---------------------------------------------------
t/ELM........................ok
t/ESEfinder..................error is 0
t/ESEfinder..................ok
        10/12 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Genewise...................ok
        2/51 skipped:
t/GOR4.......................ok
        10/13 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/HNN........................ok
        10/13 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/MitoProt...................ok
        5/8 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/protgraph..................Class::AutoClass or Clone not installed.
This means that the module is not usable. Skipping tests at
t/protgraph.t line 23.
t/RefSeq.....................ok
        10/13 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/RemoteBlast................ok
        4/6 skipped: to avoid timeout
t/SeqIO......................XML::DOM::XPath not found - skipping
interpro tests
XML::SAX::Base or XML::SAX or XML::SAX::Writer not found - skipping
BSML_SAX tests
t/SeqIO......................ok
t/simpleGOparser.............ok 88/101Use of uninitialized value in hash
element at /home/te07/bioperl-1.5.0-
RC2/blib/lib/Bio/Ontology/OntologyStore.pm line 263, <GEN3> line 11.
t/Sopma......................ok
        12/15 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Taxonomy...................ok
        7/8 skipped: to avoid blocking
t/tutorial...................ok 18/21Use of uninitialized value in print
at /home/te07/bioperl-1.5.0-RC2/blib/lib/bptutorial.pl line 4039,
<GEN21> line 934.

All tests successful, 114 subtests skipped.
Files=193, Tests=8942, 959 wallclock secs (108.35 cusr +  7.82 csys =
116.17 CPU)