[Bioperl-l] Make test fails

[Ryan Golhar]

I just updated my copy of bioperl live from cvs and when I do a 'make
test', it fails miserably.  Here's the relevant output:

t/DB.........................FAILED test 24
        Failed 1/84 tests, 98.81% okay
t/DBCUTG.....................ok
        22/24 skipped: tests which require remote servers - set env
variable BIO
PERLDEBUG to test
t/DBFasta....................ok
t/DNAMutation................ok
t/Domcut.....................ok
        22/25 skipped: tests which require remote servers - set env
variable BIO
PERLDEBUG to test
t/ECnumber...................ok
t/ELM........................
-------------------- WARNING ---------------------
MSG: Bio::Tools::Analysis::Protein::ELM Request Error:
400 (Bad Request) URL must be absolute
Client-Date: Wed, 31 Aug 2005 04:23:10 GMT



---------------------------------------------------
ok
t/embl.......................
-------------------- WARNING ---------------------
MSG: Bio::PrimarySeq=HASH(0x9f74ff8) is not a SeqI compliant sequence
object!
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: test is not a SeqI compliant sequence object!
---------------------------------------------------
ok
t/EMBL_DB....................ok
t/ESEfinder..................error is 0
ok
        10/12 skipped: tests which require remote servers - set env
variable BIO
PERLDEBUG to test
t/FeatureIO..................
-------------------- WARNING ---------------------
MSG: '##feature-ontology' directive handling not yet implemented
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: '##attribute-ontology' directive handling not yet implemented
---------------------------------------------------

-------------------- WARNING ---------------------
MSG: '##source-ontology' directive handling not yet implemented
---------------------------------------------------
ok
t/Index......................
-------------------- WARNING ---------------------
MSG: overwriting a current value stored for AJ288898

---------------------------------------------------

-------------------- WARNING ---------------------
MSG: overwriting a current value stored for AI129902

---------------------------------------------------

-------------------- WARNING ---------------------
MSG: overwriting a current value stored for BAB68554

---------------------------------------------------
ok
t/protgraph..................doing subgraphs
|||||||in subgraph - size30
in subgraph - size33
in subgraph - size3
in subgraph - size3
in subgraph - size5
Can't call method "object_id" on unblessed reference at t/protgraph.t
line 81, <
GEN1> line 82.
dubious
        Test returned status 25 (wstat 6400, 0x1900)
        after all the subtests completed successfully
t/Spidey.....................Global symbol "$exon_num" requires explicit
package
 name at /tmp/bioperl-live/blib/lib/Bio/Tools/Spidey/Results.pm line
309.
Global symbol "$gen_start" requires explicit package name at
/tmp/bioperl-live/b
lib/lib/Bio/Tools/Spidey/Results.pm line 309.
Global symbol "$gen_stop" requires explicit package name at
/tmp/bioperl-live/bl
ib/lib/Bio/Tools/Spidey/Results.pm line 309.
Global symbol "$cdna_start" requires explicit package name at
/tmp/bioperl-live/
blib/lib/Bio/Tools/Spidey/Results.pm line 309.
Global symbol "$cdna_stop" requires explicit package name at
/tmp/bioperl-live/b
lib/lib/Bio/Tools/Spidey/Results.pm line 309.


Any idea why I'm getting these errors?  Should I blow away my
bioperl-live directory and checkout a whole new version?

My spidey modules shouldn't be failing...my last update to it was
working fine...

Ryan