[Biojava-dev] BioJava Install
nicolas desreumaux
nicolas.desreumaux at obs-banyuls.fr
Fri Mar 28 12:30:06 UTC 2008
Dear All,
We have a problem to install BioJava on MacOs 10.4
Below errors :
---------------------------------------------------------
Buildfile: build.xml
init:
[echo] Building biojava-1.5
[echo] Java Home: /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0/Home
[echo] JUnit present: ${junit.present}
[echo] JUnit supported by Ant: true
[echo] HSQLDB driver present: ${sqlDriver.hsqldb}
[echo] XSLT support: true
prepare:
prepare-tests:
prepare-biojava:
compile-biojava:
[javac] Compiling 366 source files to /Users/pierre/BioJava1.5-all/biojava-1.5/ant-build/classes/biojava
[javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:316: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:381: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:451: cannot find symbol
[javac] symbol : variable TYPE_OBJECT
[javac] location: class org.biojava.utils.bytecode.CodeUtils
[javac] CodeClass c_baseClass = CodeUtils.TYPE_OBJECT;
[javac] ^
[javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:462: cannot find symbol
[javac] symbol : variable TYPE_OBJECT
[javac] location: class org.biojava.utils.bytecode.CodeUtils
[javac] = CodeUtils.TYPE_OBJECT.getConstructor(CodeUtils.EMPTY_LIST);
[javac] ^
[javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:497: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:507: cannot find symbol
[javac] symbol : method getFields()
[javac] location: interface org.biojava.utils.bytecode.CodeClass
[javac] for(Iterator fi = c_ourTemplate.getFields().iterator();
[javac] ^
[javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:537: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:539: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/bio/seq/projection/ProjectionEngine.java:541: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:246: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:275: cannot find symbol
[javac] symbol : method forMethod(java.lang.reflect.Method)
[javac] location: class org.biojava.utils.bytecode.IntrospectedCodeClass
[javac] CodeMethod m_getChild = IntrospectedCodeClass.forMethod(m);
[javac] ^
[javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:293: cannot find 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_ourType));
[javac] ^
[javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:308: cannot find 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_ourType));
[javac] ^
[javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:339: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:345: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:354: cannot find 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] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:376: cannot find symbol
[javac] symbol : variable TYPE_OBJECT
[javac] location: class org.biojava.utils.bytecode.CodeUtils
[javac] CodeUtils.TYPE_OBJECT,
[javac] ^
[javac] /Users/pierre/BioJava1.5-all/biojava-1.5/src/org/biojava/utils/walker/WalkerFactory.java:406: cannot find symbol
[javac] symbol : variable TYPE_OBJECT
[javac] location: class org.biojava.utils.bytecode.CodeUtils
[javac] CodeUtils.TYPE_OBJECT,
[javac] ^
[javac] Note: Some input files use or override a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] 18 errors
BUILD FAILED
/Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details.
Total time: 17 seconds
gwenael-piganeaus-Computer:~/BioJava1.5-all/biojava-1.5 pierre$ ant runtests>tests.txt
BUILD FAILED
/Users/pierre/BioJava1.5-all/biojava-1.5/build.xml:266: Compile failed; see the compiler error output for details.
Total time: 11 seconds
---------------------------------------------------------
What can I do to avoid these errors ?
Thanks.
Best regards,
Nicolas Desreumaux
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