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

Wed Jan 14 13:24:19 UTC 2009

On Jan 14, 2009, at 12:48 AM, Nathan S. Watson-Haigh wrote:

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> Been away from Perl for a while now, but still try to keep up-to- 
> date with the mailing list.
>
> Anyway, since Chris mentioned that he'd not recieved much feedback  
> on the latest RC's, I thought I'd
> checkout the trunk on a clean Ubuntu 8.04 Desktop.
>
> Opting not to install any optional deps or scripts and no network  
> tests I get a non-zero exit status
> due to bad plan in t/SearchIO/blastxml (sorry for not putting the  
> exact output as I'm running the
> tests on another machine):
> Parse errors: Bad plan.  You planned 298 tests but ran 130.

That's an odd one but it may be a test miscount.  I'll double-check.   
I tried this on a clean Ubuntu 8.10 yesterday (perl 5.10) and had no  
problems beyond having to use 'sudo' to install the Data::Stag  
requirement.

> I had to resort to installing all dependencies to get this past this  
> hurdle. However, after doing
> so, I now get a non-zero exit status for t/seqFeature/SeqFeature:
> Failed test: 86
> Non-zero exit status: 1
>
> Basically, I get an exception about acc AF032048 does not exist.
> In addition, the test at line 322 gives a different sequence to that  
> being expected....the last 4
> aa's appear to have be replaced by ~20 X's
>
> Anyway, thought I'd chirp in before the RC3 is tagged.
>
> Nath

Okay, will look into that one (an odd one as well, but Dave reported  
something with the same batch of tests; different fails though.   
Thanks Nathan (and good to hear from you).

chris

> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
> - --
> - --------------------------------------------------------
> Dr. Nathan S. Watson-Haigh
> OCE Post Doctoral Fellow
> CSIRO Livestock Industries
> Queensland Bioscience Precinct
> St Lucia, QLD 4067
> Australia
>
> Tel: +61 (0)7 3214 2922
> Fax: +61 (0)7 3214 2900
> Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
> - --------------------------------------------------------
>
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