Bioperl and Perl 5.10

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So far only a few problems have been detected with perl 5.10 and BioPerl. The following is a quick run using a fresh build of perl 5.10 on Mac OS X 10.5.1 (Intel); all prereqs were preinstalled as well as DBI and DBD:mysql with MySQL 5.0.45, so this process may gloss over some installation issues with Build.PL.

Contents

Installation issues

bioperl-live

perl 5.10 specific

  • BioGraphics.t (filed as Issue #2457) Lincoln has fixed in Subversion
  ...
   ok 32
   ok 33
   ok 34
   ok 35
   
   #   Failed test at t/BioGraphics.t line 49.
   #          got: '7'
   #     expected: '5'
   # Looks like you failed 1 test of 35.
    Dubious, test returned 1 (wstat 256, 0x100)
    Failed 1/35 subtests
  • Exception due to uninstalled prerequisite Graph::Directed is not being caught properly. These tests gets skipped like they should under Perl 5.8. Actually, other tests where Graph::Directed is required are properly skipped (e.g. GOterm.t), so those might illuminate the problem. Now fixed in Subversion
t/SeqFeatAnnotated..............ok 1/26Bio::OntologyIO: obo cannot be found  
Exception 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::OntologyIO::obo. Can't locate Graph/Directed.pm in @INC (@INC contains: t/lib /Users/dave/src/bioperl-
live/blib/lib /Users/dave/src/bioperl-live/blib/arch /Users/dave/src/bioperl-live /usr/local/lib/perl5/5.10.0/darwin-2level 
/usr/local/lib/perl5/5.10.0 /usr/local/lib/perl5/site_perl/5.10.0/darwin-2level /usr/local/lib/perl5/site_perl/5.10.0 .)
at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm line 118.
BEGIN failed--compilation aborted at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm line 118.
Compilation failed in require at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/OBOEngine.pm line 74.
BEGIN failed--compilation aborted at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/OBOEngine.pm line 74.
Compilation failed in require at /Users/dave/src/bioperl-live/blib/lib/Bio/OntologyIO/obo.pm line 88.
BEGIN failed--compilation aborted at /Users/dave/src/bioperl-live/blib/lib/Bio/OntologyIO/obo.pm line 88.
Compilation failed in require at /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm line 420.

STACK: Error::throw
STACK: Bio::Root::Root::throw /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:357
STACK: Bio::Root::Root::_load_module /Users/dave/src/bioperl-live/blib/lib/Bio/Root/Root.pm:422
STACK: Bio::OntologyIO::_load_format_module /Users/dave/src/bioperl-live/blib/lib/Bio/OntologyIO.pm:260
STACK: Bio::OntologyIO::new /Users/dave/src/bioperl-live/blib/lib/Bio/OntologyIO.pm:170
STACK: Bio::Ontology::OntologyStore::get_ontology /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/OntologyStore.pm:225
STACK: Bio::SeqFeature::Annotated::primary_tag /Users/dave/src/bioperl-live/blib/lib/Bio/SeqFeature/Annotated.pm:654
STACK: Bio::SeqFeature::Annotated::from_feature /Users/dave/src/bioperl-live/blib/lib/Bio/SeqFeature/Annotated.pm:287
STACK: Bio::SeqFeature::Annotated::_initialize /Users/dave/src/bioperl-live/blib/lib/Bio/SeqFeature/Annotated.pm:247
STACK: Bio::SeqFeature::Annotated::new /Users/dave/src/bioperl-live/blib/lib/Bio/SeqFeature/Annotated.pm:210
STACK: t/SeqFeatAnnotated.t:42
-----------------------------------------------------------

For more information about the OntologyIO system please see the docs.
This includes ways of checking for formats at compile time, not run time
Can't call method "next_ontology" on an undefined value at /Users/dave/src/bioperl-live/blib/lib/Bio/Ontology/OntologyStore.pm line 229.
# Looks like you planned 26 tests but only ran 5.
# Looks like your test died just after 5.
t/SeqFeatAnnotated..............dubious                                      
	Test returned status 255 (wstat 65280, 0xff00)
DIED. FAILED tests 6-26
	Failed 21/26 tests, 19.23% okay
  • DB.t. Now fixed in Subversion.
   ...
   ok 105 - use Bio::DB::EntrezGene;
   ok 106
   Not a HASH reference at /Users/cjfields/src/core/bioperl-live/Bio/SeqIO/entrezgene.pm line 372, <IN> line 2.
   # Looks like you planned 116 tests but only ran 106.
   # Looks like your test died just after 106.
    Dubious, test returned 255 (wstat 65280, 0xff00)
    Failed 10/116 subtests 
   
   Test Summary Report
   -------------------
   t/DB.t (Wstat: 65280 Tests: 106 Failed: 0)
     Non-zero exit status: 255
     Parse errors: Bad plan.  You planned 116 tests but ran 106.
   Files=1, Tests=106, 25 wallclock secs ( 0.03 usr  0.01 sys +  1.61 cusr  0.36 csys =  2.01 CPU)
   Result: FAIL
   Failed 1/1 test programs. 0/106 subtests failed.
  • entrezgene.t Now fixed in Subversion.
   ...
   ok 643
   ok 644
   ok 645
   ok 646
   ok 647
   ok 648 - correct number of loops for T15
   Not a HASH reference at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/SeqIO/entrezgene.pm line 491, <IN> line 15.
   # Looks like you planned 1422 tests but only ran 648.
   # Looks like your test died just after 648.
    Dubious, test returned 255 (wstat 65280, 0xff00)
    Failed 774/1422 subtests 
   
   Test Summary Report
   -------------------
   t/entrezgene.t (Wstat: 65280 Tests: 648 Failed: 0)
     Non-zero exit status: 255
     Parse errors: Bad plan.  You planned 1422 tests but ran 648.
   Files=1, Tests=648,  2 wallclock secs ( 0.10 usr  0.02 sys +  1.35 cusr  0.05 csys =  1.52 CPU)
   Result: FAIL
   Failed 1/1 test programs. 0/648 subtests failed.

Other issues (all perl versions)

  • Repeated "Encountered CODE ref, using dummy placeholder at /usr/local/lib/perl5/5.10.0/darwin-2level/Data/Dumper.pm line 190." warnings. May be specific to my perl build. [I'm seeing the same error on a PPC Mac. -Dave Messina 16:22, 19 December 2007 (EST)] This appears to be a problem in Module::Build.
  • Tests were run with a new CVS checkout with all prereqs and bioperl-ext modules installed.
   Test Summary Report
   -------------------
   t/Annotation.t                (Wstat: 0 Tests: 112 Failed: 0)
     TODO passed:   96
   t/BioGraphics.t               (Wstat: 256 Tests: 35 Failed: 1)
     Failed test number(s):  4
     Non-zero exit status: 1
   t/DB.t                        (Wstat: 65280 Tests: 106 Failed: 0)
     Non-zero exit status: 255
     Parse errors: Bad plan.  You planned 116 tests but ran 106.
   t/DBCUTG.t                    (Wstat: 1024 Tests: 33 Failed: 4)
     Failed test number(s):  29-31, 33
     Non-zero exit status: 4
   t/RNA_SearchIO.t              (Wstat: 2048 Tests: 496 Failed: 8)
     Failed test number(s):  291, 338, 372-374, 395, 455, 486
     Non-zero exit status: 8
   t/Spidey.t                    (Wstat: 65280 Tests: 3 Failed: 0)
     Non-zero exit status: 255
     Parse errors: Bad plan.  You planned 26 tests but ran 3.
   t/entrezgene.t                (Wstat: 65280 Tests: 648 Failed: 0)
     Non-zero exit status: 255
     Parse errors: Bad plan.  You planned 1422 tests but ran 648.
   Files=255, Tests=17416, 381 wallclock secs ( 3.29 usr  1.58 sys + 137.04 cusr 13.41 csys = 155.32 CPU)
   Result: FAIL
   Failed 7/255 test programs. 14/17416 subtests failed.
  • RNA_SearchIO.t tests need to be updated to reflect recent changes to Bio::SearchIO-related modules. Now fixed in Subversion.
  • DBCUTG.t: Now fixed in Subversion.
   ...
   ok 26
   ok 27
   ok 28
   Use of uninitialized value $sp in substitution (s///) at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/DB/CUTG.pm line 240.
   Use of uninitialized value $sp in concatenation (.) or string at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/DB/CUTG.pm line 244.
   Use of uninitialized value $name in pattern match (m//) at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/DB/CUTG.pm line 151.
   Use of uninitialized value in concatenation (.) or string at /Users/cjfields/src/core/bioperl-live/blib/lib/Bio/DB/CUTG.pm line 256.
   
   --------------------- WARNING ---------------------
   MSG: probable parsing error - should be 21 entries for 20aa + stop codon
   ---------------------------------------------------
   
   --------------------- WARNING ---------------------
   MSG: cds_count value is undefined, returning 0
   ---------------------------------------------------
   not ok 29
   
   #   Failed test at t/DBCUTG.t line 68.
   #     '0'
   #         >
   #     '600'
   not ok 30
   
   #   Failed test at t/DBCUTG.t line 69.
   #     '0'
   #         >
   #     '1'
   
   --------------------- WARNING ---------------------
   MSG: coding gc values aren't defined, returning 0
   ---------------------------------------------------
   not ok 31
   
   #   Failed test at t/DBCUTG.t line 70.
   Use of uninitialized value $got in numeric lt (<) at t/DBCUTG.t line 71.
   ok 32
   
   --------------------- WARNING ---------------------
   MSG: probable parsing error - should be 21 entries for 20aa + stop codon
   ---------------------------------------------------
   not ok 33
   
   #   Failed test at t/DBCUTG.t line 79.
   #          got: 'unknown'
   #     expected: 'Homo sapiens'
   # Looks like you failed 4 tests of 33.
    Dubious, test returned 4 (wstat 1024, 0x400)
    Failed 4/33 subtests 
   
   Test Summary Report
   -------------------
   t/DBCUTG.t (Wstat: 1024 Tests: 33 Failed: 4)
     Failed test number(s):  29-31, 33
     Non-zero exit status: 4
   Files=1, Tests=33,  3 wallclock secs ( 0.02 usr  0.01 sys +  0.44 cusr  0.09 csys =  0.56 CPU)
   Result: FAIL
   Failed 1/1 test programs. 4/33 subtests failed.
  • Spidey.t Now fixed in Subversion.
   ...
   1..26
   ok 1 - use Bio::Tools::Spidey::Results;
   ok 2
   ok 3
   Can't call method "sub_SeqFeature" on an undefined value at t/Spidey.t line 24, <GEN1> line 170.
   # Looks like you planned 26 tests but only ran 3.
   # Looks like your test died just after 3.
    Dubious, test returned 255 (wstat 65280, 0xff00)
    Failed 23/26 subtests 
   
   Test Summary Report
   -------------------
   t/Spidey.t (Wstat: 65280 Tests: 3 Failed: 0)
     Non-zero exit status: 255
     Parse errors: Bad plan.  You planned 26 tests but ran 3.
   Files=1, Tests=3,  0 wallclock secs ( 0.01 usr  0.00 sys +  0.19 cusr  0.03 csys =  0.23 CPU)
   Result: FAIL
   Failed 1/1 test programs. 0/3 subtests failed.

bioperl-db

No apparent issues: all tests pass using DBI and DBD::mysql, Mac OS X Leopard, and the latest BioSQL checkout.

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