[Bioperl-l] About to tag the last RC...

[Dave Messina]

Grabbed the trunk and tried again.

This time, missing dependencies were correctly fetched and installed.

I'm still getting the HIV error:

t/RemoteDB/HIV/HIV...........................23/30
#   Failed test 'get HXB2 in a stream by accession'
#   in t/RemoteDB/HIV/HIV.t at line 79.
# died: Bio::WebError::Exception (
# ------------- EXCEPTION: Bio::WebError::Exception -------------
# MSG: Unparsed failure at
/Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm line 275.
#
# VALUE: An empty string ("")
# STACK: Error::throw
# STACK: Bio::Root::Root::throw
/Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357
# STACK: Bio::DB::HIV::get_request
/Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:277
# STACK: Bio::DB::HIV::get_seq_stream
/Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:396
# STACK: Bio::DB::HIV::get_Stream_by_acc
/Users/dave/src/bioperl-live/blib/lib/Bio/DB/HIV.pm:491
# STACK: Test::Exception::lives_ok t/RemoteDB/HIV/HIV.t:79
# STACK: t/RemoteDB/HIV/HIV.t:79
# ---------------------------------------------------------------
# )
# Looks like you failed 1 test of 30.
t/RemoteDB/HIV/HIV........................... Dubious, test returned 1
(wstat 256, 0x100)
 Failed 1/30 subtests
(less 7 skipped subtests: 22 okay)


I also got a new warning, even though the test passed:

t/Tree/TreeIO/svggraph.......................1/4 Use of uninitialized value
in join or string at /Library/Perl/5.8.8/SVG/Element.pm line 1195, <GEN0>
line 1.
t/Tree/TreeIO/svggraph.......................ok



And then finally, check out the SeqFeature test parse errors in the summary:

Test Summary Report
-------------------
t/RemoteDB/DB                            (Wstat: 256 Tests: 116 Failed: 1)
  Failed test:  104
  Non-zero exit status: 1
t/RemoteDB/GDB                           (Wstat: 2048 Tests: 12 Failed: 8)
  Failed tests:  4-7, 9-12
  Non-zero exit status: 8
t/RemoteDB/HIV/HIV                       (Wstat: 256 Tests: 30 Failed: 1)
  Failed test:  23
  Non-zero exit status: 1
t/Root/RootIO                            (Wstat: 65280 Tests: 30 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 31 tests but ran 30.
t/SeqFeature/SeqFeature                  (Wstat: 0 Tests: 350 Failed: 136)
  Failed tests:  85-209, 209-210, 210-211, 211-212, 212-213
                213-214, 214
  Parse errors: Tests out of sequence.  Found (79) but expected (81)
                Tests out of sequence.  Found (80) but expected (82)
                Tests out of sequence.  Found (81) but expected (83)
                Tests out of sequence.  Found (82) but expected (84)
                Tests out of sequence.  Found (83) but expected (85)
Displayed the first 5 of 271 TAP syntax errors.
Re-run prove with the -p option to see them all.
Files=322, Tests=16672, 567 wallclock secs ( 3.70 usr  2.11 sys + 112.37
cusr 17.65 csys = 135.83 CPU)
Result: FAIL
Failed 5/322 test programs. 146/16672 subtests failed.
116.460u 20.044s 9:28.64 24.0% 0+0k 22+957io 2pf+0w
Exit 255


All the SeqFeature tests passed; I wonder if the temporary 404 glitch was
responsible:

t/SeqFeature/FeatureIO.......................ok
t/SeqFeature/Location........................ok
t/SeqFeature/LocationFactory.................ok
t/SeqFeature/Primer..........................ok
t/SeqFeature/Range...........................ok
t/SeqFeature/RangeI..........................ok
t/SeqFeature/SeqAnalysisParser...............ok
t/SeqFeature/SeqFeatAnnotated................1/34
--------------------- WARNING ---------------------
MSG: [1/5] tried to fetch
http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo?rev=HEAD,
but server threw 404.  retrying...
---------------------------------------------------
t/SeqFeature/SeqFeatAnnotated................ok
t/SeqFeature/SeqFeatCollection...............ok
t/SeqFeature/SeqFeature...................... All 214 subtests passed
t/SeqFeature/SeqFeaturePrimer................ok
t/SeqFeature/Unflattener.....................ok
t/SeqFeature/Unflattener2....................ok



Dave