[Bioperl-l] About to tag the last RC...
Nathan S. Watson-Haigh
nathan.watson-haigh at csiro.au
Wed Jan 14 06:48:39 UTC 2009
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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.
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
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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