[Bioperl-l] Re: [Bioperl-guts-l] real module issues
Ryan Marsh
me@ryanmarsh.com
07 Oct 2002 03:52:30 -0500
Thanks very much for your answers. I found the DB_File package and
things went much smoother. The SimpleAlign and BioGraphics still failed
but you said that's ok. Everything is installed now and I'm going to try
a few small example apps to make sure everything works properly.
Thanks again,
-ryan
On Sun, 2002-10-06 at 09:34, Jason Stajich wrote:
> Thanks Ryan - see below.
>
> On 6 Oct 2002, Ryan Marsh wrote:
>
> > I've got some very serious module install problems with bioperl. I've
> > done plenty of googling for possible solutions with none found. I am
> > using a normal install of Red Hat 8 (but I had the same problems on
> > 7.3). BioGraphics is the only test that I can't reasonably blame on
> > bioperl, the GD perl module is well known to be broke on some common
> > linux distros including Red Hat and Suse. As far as GD goes, the problem
> > reports are many, the answers are few. I can find no reason why the
> > SimpleAlign and Index test fail. Will someone help me resolve this
> > problem?
> >
>
> Actually the SimpleAlign and BioGraphics failings are safe to ignore.
> They have to do with things on our end wrt the tests but not the
> correctness of the modules.
>
> SimpleAlign has to do with bad assumptions on our part about the order of
> hash keys - perl 5.8.0 uses a different hashing function so the order is
> different. This has been fixed in the current live code.
>
> The biographics problems are safe to ignore this is due to different
> combinations of GD and libgd which Lincoln didn't see before the release.
> It should also be corrected now in the current live code.
>
> The Index failings seem to be because of missing DB_File. And/or may have
> to do with you re-running the make test and things not getting cleaned up
> from an unsucessful fail. We should add these tempfiles to the make clean
> cleanup procedure I guess. You do, however need DB_File, -- I thought it
> was definitely standard in all modern Perl distros, apparently not?
>
> > See the output:
> >
> > t/AAChange................ok
> > t/AAReverseMutate.........ok
> > t/AlignIO.................ok
> > t/Allele..................ok
> > t/Alphabet................ok
> > t/Annotation..............ok
> > t/Biblio..................ok
> > t/Biblio_biofetch.........ok
> > t/BiblioReferences........ok
> > t/BioDBGFF................ok
> > t/BioFetch_DB.............ok
> > t/BioGraphics.............FAILED tests 1-3
> > Failed 3/14 tests, 78.57% okay
> > t/BlastIndex..............ok 2/13File
> > /root/.cpan/build/bioperl-1.0.2/t/data/multi_blast.bls already indexed.
> > Skipping...
> > t/BlastIndex..............FAILED test 3
> > Failed 1/13 tests, 92.31% okay
> > t/BPbl2seq................ok
> > t/BPlite..................ok
> > t/BPpsilite...............ok
> > t/Chain...................ok
> > t/Clustalw................ok 4/10Clustalw program not found. Skipping
> > tests 5 to 10.
> > t/Clustalw................ok
> > t/CodonTable..............ok
> > t/consed..................ok
> > t/CytoMap.................ok
> > t/DB......................ok
> > t/DBFasta.................ok
> > t/DNAMutation.............ok
> > t/EMBL_DB.................ok
> > t/EMBOSS..................ok
> > t/ePCR....................ok
> > t/Exception...............ok
> > t/flat....................DB_File not loaded. This means flat.t test
> > cannot be executed. Skipping
> > t/flat....................ok 7/7No root path(s) specified
> > at /root/.cpan/build/bioperl-1.0.2/blib/lib/Bio/Root/IO.pm line 613
> > t/flat....................ok
> > t/game....................ok
> > t/GDB.....................ok
> > t/Genpred.................ok
> > t/GFF.....................ok
> > t/hmmer...................ok
> > t/Index...................
> > ------------- EXCEPTION -------------
> > MSG: This index file is from version [0.1] - You need to rebuild it to
> > use module version [0.2]
> > STACK Bio::Index::Abstract::_type_and_version
> > /root/.cpan/build/bioperl-1.0.2/blib/lib/Bio/Index/Abstract.pm:486
> > STACK Bio::Index::Abstract::open_dbm
> > /root/.cpan/build/bioperl-1.0.2/blib/lib/Bio/Index/Abstract.pm:407
> > STACK Bio::Index::Abstract::new
> > /root/.cpan/build/bioperl-1.0.2/blib/lib/Bio/Index/Abstract.pm:151
> > STACK Bio::Index::AbstractSeq::new
> > /root/.cpan/build/bioperl-1.0.2/blib/lib/Bio/Index/AbstractSeq.pm:91
> > STACK toplevel t/Index.t:30
> >
> > --------------------------------------
> > t/Index...................dubious
> > Test returned status 255 (wstat 65280, 0xff00)
> > DIED. FAILED tests 1-12
> > Failed 12/12 tests, 0.00% okay
> > t/largefasta..............ok
> > t/largepseq...............ok
> > t/LinkageMap..............ok
> > t/LiveSeq.................ok
> > t/LocatableSeq............ok
> > t/Location................ok
> > t/lucy....................ok
> > t/Map.....................ok
> > t/MapIO...................ok
> > t/MicrosatelliteMarker....ok
> > t/multiple_fasta..........ok
> > t/Mutation................ok
> > t/Mutator.................ok
> > t/Node....................ok
> > t/OddCodes................ok
> > t/Perl....................ok
> > t/phd.....................ok
> > t/primaryqual.............ok
> > t/PrimarySeq..............ok
> > t/qual....................ok
> > t/RandomTreeFactory.......ok
> > t/Range...................ok
> > t/RangeI..................ok
> > t/RefSeq..................ok
> > t/RemoteBlast.............ok 2/6Skipping submitting remote BLAST to
> > avoid Time-out
> > t/RemoteBlast.............ok
> > 4/6 skipped: to avoid timeout
> > t/RestrictionEnzyme.......ok
> > t/RNAChange...............ok
> > t/RootI...................ok
> > t/scf.....................ok
> > t/SearchDist..............ok
> > t/SearchIO................ok
> > t/Seq.....................ok
> > t/SeqAnal.................ok
> > t/SeqAnalysisParser.......ok
> > t/SeqDiff.................ok
> > t/SeqFeature..............ok
> > t/SeqIO...................ok
> > t/SeqPattern..............ok
> > t/SeqStats................ok
> > t/SeqUtils................ok
> > t/seqwithquality..........ok
> > t/Sigcleave...............ok
> > t/Sim4....................ok
> > t/SimilarityPair..........ok
> > t/SimpleAlign.............FAILED test 18
> > Failed 1/53 tests, 98.11% okay
> > t/Species.................ok
> > t/StandAloneBlast.........ok
> > t/StateMachine............ok
> > t/StructIO................ok
> > t/Structure...............ok
> > t/Swiss...................ok
> > t/Symbol..................ok
> > t/TCoffee.................ok 4/16tcoffee program not found. Skipping
> > tests 5 to 16.
> > t/TCoffee.................ok
> > t/Tempfile................ok
> > t/Tools...................ok
> > t/TreeIO..................ok
> > t/trim....................ok
> > t/Variation_IO............ok
> > t/XEMBL_DB................ok
> > Failed Test Stat Wstat Total Fail Failed List of Failed
> > -------------------------------------------------------------------------------
> > t/BioGraphics.t 14 3 21.43% 1-3
> > t/BlastIndex.t 13 1 7.69% 3
> > t/Index.t 255 65280 12 12 100.00% 1-12
> > t/SimpleAlign.t 53 1 1.89% 18
> > 4 subtests skipped.
> > Failed 4/94 test scripts, 95.74% okay. 17/3279 subtests failed, 99.48%
> > okay.
> > make: *** [test_dynamic] Error 29
> > /usr/bin/make test -- NOT OK
> > Running make install
> > make test had returned bad status, won't install without force
> >
> > Thanks,
> > -ryan
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
>
--
Humans are the unfortunate result of of a local maximum in the
fitness landscape.
www.ryanmarsh.com