[Biojava-l] Build errors

Andy Hammer facemann at yahoo.com
Fri Sep 12 21:31:29 EDT 2003 

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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