[Biojava-l] Build errors
Schreiber, Mark
mark.schreiber at agresearch.co.nz
Sat Sep 13 00:38:28 EDT 2003
Looks like you might not have the bytecode.jar file which is odd. Do you see it in your biojava-live directory?
- Mark
-----Original Message-----
From: Andy Hammer [mailto:facemann at yahoo.com]
Sent: Sat 13/09/2003 1:31 p.m.
To: bio java
Cc:
Subject: [Biojava-l] Build errors
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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