[Bioperl-l] failures on the stable branch
Rob Edwards
redwards at utmem.edu
Wed Apr 21 09:56:38 EDT 2004
There is a thread about RestrictionIO test 14 failing back in January.
http://bioperl.org/pipermail/bioperl-l/2004-January/014487.html
I couldn't repeat the error, and no one could identify why that test
failed, so it wasn't chased down. If you or anyone else has any clues
let me know. There is also not a bugzilla report for it.
Rob
On Apr 21, 2004, at 8:04 AM, Dave Howorth wrote:
> On Tue, 20 Apr 2004, Hilmar Lapp wrote:
>>> On the latest update of the stable branch if you run the test suite
>>> you
>>> get a number of failures, some of them looking troubling to the
>>> uninitiated.
>
> I was the one having trouble. As previously discussed, I've just
> installed bioperl-db/biosql with my existing bioperl 1.4 installation
> and am trying to load the GO data. It failed because of problems in 1.4
> and Hilmar advised me to get branch-1-4 from cvs.
>
> Yesterday Hilmar very kindly helped me through the process, because I'm
> a newbie to it, but it failed with the errors he described. I've just
> updated from CVS and unfortunately now get a different set of errors:
>
> Failed Test Stat Wstat Total Fail Failed List of Failed
> -----------------------------------------------------------------------
> --------
> t/DB.t 78 9 11.54% 79-87
> t/RestrictionIO.t 14 1 7.14% 10
> t/TreeIO.t 41 1 2.44% 42
> t/cigarstring.t 255 65280 3 6 200.00% 1-3
> 121 subtests skipped.
> make: *** [test_dynamic] Error 11
>
> (the full log is at the end)
>
> What I still don't know is whether the release as it stands will work
> for me or not. I don't want to break my existing installation but I
> can't get on with my current work until bioperl-db/biosql is working.
>
> Do the DB failures matter?
>
> RestrictionIO didn't fail yesterday. It does now. But I'm pretty sure I
> don't need it.
>
> TreeIO didn't fail yesterday. It does now. And I do have existing code
> that uses it.
>
> I don't use cigarstring presently, though may do in future (DAS).
>
> I don't know what "make: *** [test_dynamic] Error 11" at the end means.
>
>
>>> Given that we point people at downloading the current stable branch
>>> as
>>> a means of getting bug fixes early, in my opinion we should not aim
>>> any
>>> lower than that on the stable branch *all* tests pass at *any* time,
>>> with no exceptions. Also, modules should not be added on the stable
>>> branch, let alone an API be altered.
>
> I'd like to second this plea. My work intersects with bioperl - there
> are certain specific parts of bioperl that are relevant to my work on
> protein structure classification and huge tranches that are irrelevant.
> I don't want to have to understand the irrelevant bits of bioperl
> just
> so I can decide whether its safe to install a broken release.
>
> It just adds insult to injury if the broken release is a patch branch
> that should be clearing test failures, not introducing new ones!
>
> Jason Stajich wrote:
>> I'll take a look at some of these this week. I might have
>> inadvertantly
>> caused some of them, not sure.
>
> That would be great; as I say, I'm stuck until I can get a working
> system.
>
> Thanks, Dave
>
>
> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
> -I/usr/lib/perl/5.6.1 -I/usr/share/perl/5.6.1 -e 'use Test::Harness
> qw(&runtests $verbose); $verbose=0; runtests @ARGV;' t/*.t
> t/AAChange...................ok
> ... ok snipped
> t/Chain......................ok
> t/cigarstring................Can't use an undefined value as an ARRAY
> reference at blib/lib/Bio/Search/Hit/GenericHit.pm line 409, <GEN1>
> line
> 434.
> dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-3
> Failed 3/3 tests, 0.00% okay
> t/ClusterIO..................ok
> ...
> t/DBCUTG.....................ok
> 20/22 skipped: tests which require remote servers - set env
> variable BIOPERLDEBUG to test
> t/DBFasta....................ok
> t/DB.........................
> FAILED tests 79-87
> Failed 9/78 tests, 88.46% okay (less 1 skipped test: 68 okay,
> 87.18%)
> t/DNAMutation................ok
> t/Domcut.....................ok
> 22/25 skipped: tests which require remote servers - set env
> variable BIOPERLDEBUG to test
> t/ECnumber...................ok
> ...
> t/ESEfinder..................ok
> 10/12 skipped: tests which require remote servers - set env
> variable BIOPERLDEBUG to test
> t/est2genome.................ok
> ...
> t/GDB........................ok
> t/GeneCoordinateMapper.......
> -------------------- WARNING ---------------------
> MSG: sorted sublocation array requested but root location doesn't
> define
> seq_id (at least one sublocation does!)
> ---------------------------------------------------
>
> -------------------- WARNING ---------------------
> MSG: sorted sublocation array requested but root location doesn't
> define
> seq_id (at least one sublocation does!)
> ---------------------------------------------------
> Use of uninitialized value in concatenation (.) or string at
> blib/lib/Bio/Coordinate/GeneMapper.pm line 814.
> ok
> t/Geneid.....................ok
> t/Genewise...................ok
> 2/51 skipped:
> t/Genomewise.................ok
> t/Genpred....................ok
> t/GFF........................Filehandle Symbol::GEN0 opened only for
> output at blib/lib/Bio/Root/IO.pm line 440.
> Filehandle Symbol::GEN1 opened only for output at
> blib/lib/Bio/Root/IO.pm line 440.
> ok
> t/GOR4.......................ok
> 8/11 skipped: tests which require remote servers - set env
> variable BIOPERLDEBUG to test
> t/GOterm.....................ok
> t/GuessSeqFormat.............ok
> t/hmmer......................ok
> t/HNN........................ok
> 10/13 skipped: tests which require remote servers - set env
> variable BIOPERLDEBUG to test
> t/Index......................ok
> ...
> t/MitoProt...................ok
> 5/8 skipped: tests which require remote servers - set env
> variable BIOPERLDEBUG to test
> t/Molphy.....................ok
> ...
> t/RefSeq.....................ok
> 10/13 skipped: tests which require remote servers - set env
> variable BIOPERLDEBUG to test
> t/Registry...................DB_File and BerkeleyDB not found. Skipping
> DB_File tests
> ok
> t/Relationship...............ok
> t/RelationshipType...........ok
> t/RemoteBlast................ok
> 4/6 skipped: to avoid timeout
> t/RepeatMasker...............ok
> t/RestrictionAnalysis........ok
> t/RestrictionEnzyme..........ok
> t/RestrictionIO..............Use of uninitialized value in string eq at
> blib/lib/Bio/Restriction/IO/withrefm.pm line 130, <GEN1> line 13.
> Use of uninitialized value in string eq at
> blib/lib/Bio/Restriction/IO/withrefm.pm line 130, <GEN1> line 24.
> FAILED test 10
> Failed 1/14 tests, 92.86% okay
> t/RNAChange..................ok
> ...
> t/SeqFeature.................ok
> 6/74 skipped: tests which need the Bio::DB::GenBank module
> t/SeqIO......................ok
> 3/235 skipped:
> t/SeqPattern.................ok
> ...
> t/Sopma......................ok
> 12/15 skipped: tests which require remote servers - set env
> variable BIOPERLDEBUG to test
> t/Species....................ok
> ...
> t/Taxonomy...................ok
> 7/8 skipped: to avoid blocking
> t/Tempfile...................ok
> t/Term.......................ok
> t/Tools......................ok
> t/TreeIO.....................FAILED test 42
> Failed 1/41 tests, 97.56% okay (less 1 skipped test: 39 okay,
> 95.12%)
> t/Tree.......................ok
> t/trim.......................ok
> t/tutorial...................Use of uninitialized value in print at
> blib/lib/bptutorial.pl line 4042, <GEN21> line 934.
> ok
> t/UCSCParsers................ok
> t/Unflattener2...............ok
> t/Unflattener................ok
> t/UniGene....................ok
> t/Variation_IO...............ok
> t/WABA.......................ok
> t/XEMBL_DB...................ok
> Failed 4/180 test scripts, 97.78% okay. -6/8314 subtests failed,
> 100.07%
> okay.
> Failed Test Stat Wstat Total Fail Failed List of Failed
> -----------------------------------------------------------------------
> --------
> t/DB.t 78 9 11.54% 79-87
> t/RestrictionIO.t 14 1 7.14% 10
> t/TreeIO.t 41 1 2.44% 42
> t/cigarstring.t 255 65280 3 6 200.00% 1-3
> 121 subtests skipped.
> make: *** [test_dynamic] Error 11
>
>
> --
> Dave Howorth
> MRC Centre for Protein Engineering
> Hills Road, Cambridge, CB2 2QH
> 01223 252960
>
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