[Bioperl-l] bioperl on osX 10.5

Mark Blaxter mark.blaxter at ed.ac.uk
Wed Nov 5 10:05:49 EST 2008


Hi BioPerl team

in installing BioPerl with cpan on macOSX 10.5 ( "cpan>force install S/ 
SE/SENDU/bioperl-1.5.2_102.tar.gz" ) I got these errors that looked  
more worrying than the remainder....
FYI, as I think bioperl works (or at least the bits I am using...)

thanks for all the work!
mark



------------- EXCEPTION  -------------
MSG: No flatfile fileid files in config - check the index has been  
made correctly
STACK Bio::DB::Flat::BinarySearch::read_config_file /Users/mblaxter/ 
Library/Application Support/.cpan/build/bioperl-1.5.2_102-vnU6b6/blib/ 
lib/Bio/DB/Flat/BinarySearch.pm:1288
STACK Bio::DB::Flat::BinarySearch::new /Users/mblaxter/Library/ 
Application Support/.cpan/build/bioperl-1.5.2_102-vnU6b6/blib/lib/Bio/ 
DB/Flat/BinarySearch.pm:276
STACK Bio::DB::Flat::new /Users/mblaxter/Library/Application  
Support/.cpan/build/bioperl-1.5.2_102-vnU6b6/blib/lib/Bio/DB/Flat.pm:177
STACK Bio::DB::Flat::new_from_registry /Users/mblaxter/Library/ 
Application Support/.cpan/build/bioperl-1.5.2_102-vnU6b6/blib/lib/Bio/ 
DB/Flat.pm:252
STACK (eval) /Users/mblaxter/Library/Application Support/.cpan/build/ 
bioperl-1.5.2_102-vnU6b6/blib/lib/Bio/DB/Registry.pm:164
STACK Bio::DB::Registry::_load_registry /Users/mblaxter/Library/ 
Application Support/.cpan/build/bioperl-1.5.2_102-vnU6b6/blib/lib/Bio/ 
DB/Registry.pm:163
STACK Bio::DB::Registry::new /Users/mblaxter/Library/Application  
Support/.cpan/build/bioperl-1.5.2_102-vnU6b6/blib/lib/Bio/DB/ 
Registry.pm:95
STACK toplevel t/Registry.t:72
STACK toplevel t/Registry.t:72
---------------------------------------------------
Can't call method "seq" on an undefined value at t/Registry.t line 81.
t/Registry................... Dubious, test returned 255 (wstat 65280,  
0xff00)
  Failed 6/13 subtests
t/Relationship...............ok
t/RelationshipType...........ok
t/RemoteBlast................ok
t/RepeatMasker...............ok
t/RestrictionAnalysis........ok
t/RestrictionIO..............ok
t/RootI......................ok
t/RootIO.....................ok
t/RootStorable...............ok
t/SNP........................ok
t/Scansite...................ok
t/SearchDist.................ok
t/SearchIO...................ok
t/Seg........................ok
t/Seq........................ok
t/SeqAnalysisParser..........ok
t/SeqBuilder.................ok
t/SeqDiff....................ok
t/SeqFeatCollection..........ok
t/SeqFeature.................92/211
-------------------- WARNING ---------------------
MSG: [1/5] tried to fetch http://umn.dl.sourceforge.net/sourceforge/song/sofa.definition 
, but server threw 500.  retrying...
---------------------------------------------------
[and on for 5 retrys]

at the end cpan reports:

Failed during this command:
  MKUTTER/SOAP-Lite-0.710.08.tar.gz            : make_test FAILED but  
failure ignored because 'force' in effect
  MINGYILIU/Bio-ASN1-EntrezGene-1.091.tgz      : make_test FAILED but  
failure ignored because 'force' in effect
  MHX/Convert-Binary-C-0.71.tar.gz             : make_test FAILED but  
failure ignored because 'force' in effect
  MIROD/XML-XPathEngine-0.11.tar.gz            : make_test FAILED but  
failure ignored because 'force' in effect
  SENDU/bioperl-1.5.2_102.tar.gz               : make_test FAILED but  
failure ignored because 'force' in effect

Mark Blaxter
mark.blaxter at ed.ac.uk

~ may all beings be happy ~




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