[Biojava-dev] BioJava Install
nicolas desreumaux
nicolas.desreumaux at obs-banyuls.fr
Fri Mar 28 13:48:21 UTC 2008
Hi
Thanks for your answer.
bytecode.jar is in my classpath and the other .jar too
"export CLASSPATH=/home/thomas/biojava.jar:/home/thomas/bytecode.jar:
/home/thomas/commons-cli.jar: /home/thomas/commons-collections-2.1.jar:
/home/thomas/commons-dbcp-1.1.jar:/home/thomas/commons-pool-1.1.jar:."
$CLASSPATH contains these files.
Nicolas
Mark Schreiber a écrit :
> 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
>>
>>
>
>
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