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

[Chris Fields]

I notified Mark about the failed HIV test, but it appears to be  
sporadically failing and is likely a server-side issue.  The  
svggraph.t is a warning that I think emanates from SVG::Graph, not a  
release killer but would be nice to get rid of.  I'll look through it,  
and if it isn't fixable on our end I'll notify Allen Day.

chris

On Jan 13, 2009, at 2:42 PM, Dave Messina wrote:

> 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
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