[Biojava-l] Build errors
Matthew Pocock
matthew_pocock at yahoo.co.uk
Tue Sep 30 05:12:48 EDT 2003
This usually happens because you are trying to build biojava from source
while you have an old biojava.jar in your classpath.
Matthew
Andy Hammer wrote:
>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
>
>__________________________________
>Do you Yahoo!?
>Yahoo! SiteBuilder - Free, easy-to-use web site design software
>http://sitebuilder.yahoo.com
>_______________________________________________
>Biojava-l mailing list - Biojava-l at biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>
>
>
More information about the Biojava-l
mailing list