[Bioperl-l] Re: [Bioperl-guts-l] real module issues
Jason Stajich
jason@cgt.mc.duke.edu
Sun, 6 Oct 2002 10:34:07 -0400 (EDT)
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