[Biojava-dev] BioJava Install
Mark Schreiber
markjschreiber at gmail.com
Fri Mar 28 13:20:08 UTC 2008
Hi =
It looks like you are missing the bytecode.jar from your classpath.
- Mark
On Fri, Mar 28, 2008 at 8:30 PM, nicolas desreumaux
<nicolas.desreumaux at obs-banyuls.fr> wrote:
> 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
>
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
More information about the biojava-dev
mailing list