ArrayIndexOutOfBoundsException when opening Bio::FlatFiles (bioruby gem)
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Key: JRUBY-3545
URL: http://jira.codehaus.org/browse/JRUBY-3545
Project: JRuby
Issue Type: Bug
Affects Versions: JRuby 1.1.4
Environment: Ubuntu Linux - kernel 2.6.27-11 i686
jruby 1.1.4 (ruby 1.8.6 patchlevel 114) (2008-08-28 rev 7570) [i386-java]
bio gem v1.3.0
Reporter: Robert Syme
Assignee: Thomas E Enebo
Attachments: main.rb, sn4_tiny.fasta
ArrayIndexOutOfBoundsException thrown when opening a Bio::FlatFile
Backtrace:
org.jruby.RubyHash:719:in `rehash': java.lang.ArrayIndexOutOfBoundsException:
-10
from org.jruby.RubyHash$i_method_0_0$RUBYINVOKER$rehash:-1:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:132:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:343:in `call'
from org.jruby.ast.CallNoArgNode:61:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.BlockNode:67:in `interpret'
from org.jruby.internal.runtime.methods.DefaultMethod:163:in
`interpretedCall'
from org.jruby.internal.runtime.methods.DefaultMethod:140:in `call'
from org.jruby.internal.runtime.methods.DefaultMethod:211:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:132:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:343:in `call'
from org.jruby.ast.CallNoArgNode:61:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.BlockNode:67:in `interpret'
from org.jruby.internal.runtime.methods.DefaultMethod:163:in
`interpretedCall'
from org.jruby.internal.runtime.methods.DefaultMethod:140:in `call'
from org.jruby.internal.runtime.methods.DefaultMethod:211:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:132:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:343:in `call'
from org.jruby.ast.CallNoArgNode:61:in `interpret'
from org.jruby.ast.InstAsgnNode:88:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.IfNode:110:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.BlockNode:67:in `interpret'
from org.jruby.internal.runtime.methods.DefaultMethod:163:in
`interpretedCall'
from org.jruby.internal.runtime.methods.DefaultMethod:140:in `call'
from org.jruby.internal.runtime.methods.DefaultMethod:211:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:132:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:343:in `call'
from org.jruby.ast.CallNoArgNode:61:in `interpret'
from org.jruby.ast.LocalAsgnNode:115:in `interpret'
from org.jruby.internal.runtime.methods.DefaultMethod:375:in
`assignOptArgs'
from org.jruby.internal.runtime.methods.DefaultMethod:449:in
`interpretOptArgs'
from org.jruby.internal.runtime.methods.DefaultMethod:444:in
`prepareOptOrRestArgs'
from org.jruby.internal.runtime.methods.DefaultMethod:439:in
`prepareArguments'
from org.jruby.internal.runtime.methods.DefaultMethod:384:in
`interpretArgs'
from org.jruby.internal.runtime.methods.DefaultMethod:418:in
`preInterpret'
from org.jruby.internal.runtime.methods.DefaultMethod:161:in
`interpretedCall'
from org.jruby.internal.runtime.methods.DefaultMethod:140:in `call'
from org.jruby.internal.runtime.methods.DefaultMethod:211:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:132:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:343:in `call'
from org.jruby.ast.VCallNode:82:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.IfNode:110:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.BlockNode:67:in `interpret'
from org.jruby.internal.runtime.methods.DefaultMethod:163:in
`interpretedCall'
from org.jruby.internal.runtime.methods.DefaultMethod:140:in `call'
from org.jruby.internal.runtime.methods.DefaultMethod:316:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:192:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:457:in `call'
from org.jruby.RubyClass$SpecificArityNew:551:in `call'
from org.jruby.internal.runtime.methods.DynamicMethod:168:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:180:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:445:in `call'
from org.jruby.ast.CallTwoArgNode:59:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.BlockNode:67:in `interpret'
from org.jruby.ast.IfNode:110:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.internal.runtime.methods.DefaultMethod:163:in
`interpretedCall'
from org.jruby.internal.runtime.methods.DefaultMethod:140:in `call'
from org.jruby.internal.runtime.methods.DefaultMethod:316:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:192:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:457:in `call'
from org.jruby.ast.FCallSpecialArgBlockPassNode:39:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.IfNode:110:in `interpret'
from org.jruby.ast.NewlineNode:101:in `interpret'
from org.jruby.ast.BlockNode:67:in `interpret'
from org.jruby.internal.runtime.methods.DefaultMethod:163:in
`interpretedCall'
from org.jruby.internal.runtime.methods.DefaultMethod:140:in `call'
from org.jruby.internal.runtime.methods.DefaultMethod:253:in `call'
from org.jruby.runtime.CallSite$InlineCachingCallSite:156:in
`cacheAndCall'
from org.jruby.runtime.CallSite$InlineCachingCallSite:394:in `call'
from home.rob.projects.jRuby.experiment_2.lib.main:5:in `__file__'
from home.rob.projects.jRuby.experiment_2.lib.main:-1:in `__file__'
from home.rob.projects.jRuby.experiment_2.lib.main:-1:in `load'
from org.jruby.Ruby:544:in `runScript'
from org.jruby.Ruby:457:in `runNormally'
from org.jruby.Ruby:330:in `runFromMain'
from org.jruby.Main:214:in `run'
from org.jruby.Main:100:in `run'
from org.jruby.Main:84:in `main'
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