[Biojava-l] Build errors

Schreiber, Mark mark.schreiber at agresearch.co.nz
Sat Sep 13 00:38:28 EDT 2003


Looks like you might not have the bytecode.jar file which is odd. Do you see it in your biojava-live directory?
 
- Mark
 

	-----Original Message----- 
	From: Andy Hammer [mailto:facemann at yahoo.com] 
	Sent: Sat 13/09/2003 1:31 p.m. 
	To: bio java 
	Cc: 
	Subject: [Biojava-l] Build errors
	
	

	I am getting some build errors.
	I even deleted /biojava-live and started over.
	Lastly from ./biojava-live/
	ant clean = build successful
	cvs update -d = appeared successful
	ant =
	[ahammer at westwater biojava-live]$ ant
	Buildfile: build.xml
	
	init:
	     [echo] JUnit present:                 
	${junit.present}
	     [echo] JUnit supported by Ant:          true
	
	prepare:
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build
	
	prepare-core:
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/src/main
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/classes/main
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/src/tests
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/classes/tests
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/src/demos
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/classes/demos
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/src/apps
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/classes/apps
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/src/docs
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/docs
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/docs/api
	    [mkdir] Created dir:
	/home/ahammer/downloads/biojava-live/ant-build/lib
	     [copy] Copying 1191 files to
	/home/ahammer/downloads/biojava-live/ant-build/src/main
	     [copy] Copied 23 empty directories to
	/home/ahammer/downloads/biojava-live/ant-build/src/main
	     [copy] Copying 147 files to
	/home/ahammer/downloads/biojava-live/ant-build/src/tests
	     [copy] Copied 1 empty directory to
	/home/ahammer/downloads/biojava-live/ant-build/src/tests
	     [copy] Copying 180 files to
	/home/ahammer/downloads/biojava-live/ant-build/src/demos
	     [copy] Copied 5 empty directories to
	/home/ahammer/downloads/biojava-live/ant-build/src/demos
	     [copy] Copying 2 files to
	/home/ahammer/downloads/biojava-live/ant-build/src/apps
	     [copy] Copying 15 files to
	/home/ahammer/downloads/biojava-live/ant-build/src/docs
	     [copy] Copying 1 file to
	/home/ahammer/downloads/biojava-live/ant-build/src/main
	     [copy] Copying 1 file to
	/home/ahammer/downloads/biojava-live/ant-build/src/demos
	     [copy] Copying 1 file to
	/home/ahammer/downloads/biojava-live/ant-build/src/apps
	     [copy] Copying 17 files to
	/home/ahammer/downloads/biojava-live/ant-build/classes/main
	     [copy] Copied 1 empty directory to
	/home/ahammer/downloads/biojava-live/ant-build/classes/main
	     [copy] Copying 3 files to
	/home/ahammer/downloads/biojava-live/ant-build
	
	prepare-src:
	
	compile:
	    [javac] Compiling 1091 source files to
	/home/ahammer/downloads/biojava-live/ant-build/classes/main
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/RevCompSequence.java:47:
	reference to ProjectedFeatureHolder is ambiguous, both
	class
	org.biojava.bio.seq.projection.ProjectedFeatureHolder
	in org.biojava.bio.seq.projection and class
	org.biojava.bio.seq.ProjectedFeatureHolder in
	org.biojava.bio.seq match
	    [javac]     private ProjectedFeatureHolder pfh;
	    [javac]             ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/RevCompSequence.java:65:
	reference to ProjectedFeatureHolder is ambiguous, both
	class
	org.biojava.bio.seq.projection.ProjectedFeatureHolder
	in org.biojava.bio.seq.projection and class
	org.biojava.bio.seq.ProjectedFeatureHolder in
	org.biojava.bio.seq match
	    [javac]         pfh = new
	ProjectedFeatureHolder(new
	TranslateFlipContext(this,seq,seq.length()+1,true));
	    [javac]                   ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:301:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]             
	proxyIV.add(ByteCode.make_checkcast(ourContextC));
	    [javac]                                   ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:366:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]               
	proxyIV.add(ByteCode.make_checkcast(ourContextC) );
	    [javac]                                     ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:436:
	cannot resolve symbol
	    [javac] symbol  : variable TYPE_OBJECT
	    [javac] location: class
	org.biojava.utils.bytecode.CodeUtils
	    [javac]         CodeClass c_baseClass =
	CodeUtils.TYPE_OBJECT;
	    [javac]                                          ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:447:
	cannot resolve symbol
	    [javac] symbol  : variable TYPE_OBJECT
	    [javac] location: class
	org.biojava.utils.bytecode.CodeUtils
	    [javac]                 =
	CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST);
	    [javac]                            ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:482:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]       
	revTIV.add(ByteCode.make_checkcast(c_FeatureTemplate));
	    [javac]                            ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:492:
	cannot resolve symbol
	    [javac] symbol  : method getFields ()
	    [javac] location: interface
	org.biojava.utils.bytecode.CodeClass
	    [javac]         for(Iterator fi =
	c_ourTemplate.getFields().iterator();
	    [javac]                                        ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:522:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]           
	revIV.add(ByteCode.make_checkcast(c_ourTemplate));
	    [javac]                               ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:524:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]           
	revIV.add(ByteCode.make_checkcast(c_ourContext));
	    [javac]                               ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/bio/seq/projection/ProjectionEngine.java:526:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]           
	revIV.add(ByteCode.make_checkcast(c_ourTemplate));
	    [javac]                               ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:198:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]     
	walkIV.add(ByteCode.make_checkcast(c_ourVisitor));
	    [javac]                          ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:227:
	cannot resolve symbol
	    [javac] symbol  : method forMethod
	(java.lang.reflect.Method)
	    [javac] location: class
	org.biojava.utils.bytecode.IntrospectedCodeClass
	    [javac]             CodeMethod m_getFilter =
	IntrospectedCodeClass.forMethod(m);
	    [javac]                                          
	               ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:245:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]           
	wfiv.add(ByteCode.make_checkcast(c_ourFilter));
	    [javac]                              ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:260:
	cannot resolve symbol
	    [javac] symbol  : method make_instanceof
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]       
	wrapperIV.add(ByteCode.make_instanceof(c_ourFilter));
	    [javac]                               ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:291:
	cannot resolve symbol
	    [javac] symbol  : method forMethod
	(java.lang.reflect.Method)
	    [javac] location: class
	org.biojava.utils.bytecode.IntrospectedCodeClass
	    [javac]         CodeMethod ourMeth =
	IntrospectedCodeClass.forMethod(meth);
	    [javac]                                          
	       ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:297:
	cannot resolve symbol
	    [javac] symbol  : method make_checkcast
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]       
	bodyIV.add(ByteCode.make_checkcast(c_thisFiltType));
	    [javac]                            ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:306:
	cannot resolve symbol
	    [javac] symbol  : method make_instanceof
	(org.biojava.utils.bytecode.CodeClass)
	    [javac] location: class
	org.biojava.utils.bytecode.ByteCode
	    [javac]       
	walkIV.add(ByteCode.make_instanceof(c_thisFiltType));
	    [javac]                            ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:328:
	cannot resolve symbol
	    [javac] symbol  : variable TYPE_OBJECT
	    [javac] location: class
	org.biojava.utils.bytecode.CodeUtils
	    [javac]                                         
	CodeUtils.TYPE_OBJECT,
	    [javac]                                          
	        ^
	    [javac]
	/home/ahammer/downloads/biojava-live/ant-build/src/main/org/biojava/utils/walker/WalkerFactory.java:358:
	cannot resolve symbol
	    [javac] symbol  : variable TYPE_OBJECT
	    [javac] location: class
	org.biojava.utils.bytecode.CodeUtils
	    [javac]                 CodeUtils.TYPE_OBJECT,
	    [javac]                          ^
	    [javac] 20 errors
	
	BUILD FAILED
	file:/home/ahammer/downloads/biojava-live/build.xml:278:
	Compile failed; see the compiler error output for
	details.
	
	I think last time I bothered to build was around 1.3.
	It has always worked in the past. . .
	Any ideas would be appreciated.
	
	facemann
	
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