Thanks to Michael Smoot's suggestions! I got past the 'ant'!!
'ant javadoc' in biojava-live dir succeeded. But 'ant package' failed
mid-way. Thanks for your time.
[254]% ant package
Buildfile: build.xml
init:
prepare:
[mkdir] Created dir: HOME/JAVA/biojava-live/ant-build
prepare-src:
[mkdir] Created dir: HOME/JAVA/biojava-live/ant-build/src/main
[mkdir] Created dir: HOME/JAVA/biojava-live/ant-build/classes/main
[mkdir] Created dir: HOME/JAVA/biojava-live/ant-build/src/tests
[mkdir] Created dir: HOME/JAVA/biojava-live/ant-build/classes/tests
[mkdir] Created dir: HOME/JAVA/biojava-live/reports/tests
[copy] Copying 783 files to
HOME/JAVA/biojava-live/ant-build/src/main
[copy] Copying 54 files to
HOME/JAVA/biojava-live/ant-build/src/tests
[copy] Copying 1 file to HOME/JAVA/biojava-live/ant-build/src/main
[copy] Copying 7 files to
HOME/JAVA/biojava-live/ant-build/classes/main
compile:
[javac] Modern compiler is not available - using classic compiler
[javac] Compiling 717 source files to
HOME/JAVA/biojava-live/ant-build/classes/main
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/seq/io/CharacterTokenization.java:55:
The
method org.biojava.bio.seq.io.TokenType getTokenType() declared in class
org.biojava.bio.seq.io.CharacterTokenization cannot override the method
of the same signature declared
in interface org.biojava.bio.seq.io.SymbolTokenization. They must have
the same return type.
[javac] public TokenType getTokenType() {
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/seq/io/WordTokenization.java:52:
The method org.biojava.bio.seq.io.TokenType getTokenType() declared in
class
org.biojava.bio.seq.io.WordTokenization cannot override the method of
the same signature declared in
interface org.biojava.bio.seq.io.SymbolTokenization. They must have the
same return type.
[javac] public TokenType getTokenType() {
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/seq/FramedFeature.java:52:
The
method org.biojava.bio.seq.Strand getStrand() declared in interface
org.biojava.bio.seq.FramedFeature
cannot override the method of the same signature declared in interface
org.biojava.bio.seq.StrandedFeature. They must have the same return
type.
[javac] Strand getStrand();
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/SimpleFramedFeature.java:41:
The
method org.biojava.bio.seq.StrandedFeature.Strand getStrand() declared
in class
org.biojava.bio.seq.impl.SimpleStrandedFeature cannot override the
method of the same signature
declared in interface org.biojava.bio.seq.FramedFeature. They must have
the same return type.
[javac] public class SimpleFramedFeature extends
SimpleStrandedFeature implements FramedFeature,
Frame {
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/seq/impl/SimpleFramedFeature.java:56:
The
method org.biojava.bio.seq.impl.ReadingFrame getReadingFrame() declared
in class
org.biojava.bio.seq.impl.SimpleFramedFeature cannot override the method
of the same signature declared
in interface org.biojava.bio.seq.FramedFeature. They must have the same
return type.
[javac] public ReadingFrame getReadingFrame() {
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/program/blast2html/HTMLRenderer.java:273:
class org.biojava.bio.program.blast2html.HitSummary is defined in
Blast2HTMLHandler.java. Because it is
used outside of its source file, it should be defined in a file called
"HitSummary.java".
[javac] void startSummaryTable( HitSummary oHitSummary ) {
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/program/blast2html/HTMLRenderer.java:475:
class org.biojava.bio.program.blast2html.DetailHit is defined in
Blast2HTMLHandler.java. Because it is
used outside of its source file, it should be defined in a file called
"DetailHit.java".
[javac] void writeCurrentDetail( DetailHit oDetailHit ) {
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/program/blast2html/HTMLRenderer.java:543:
class org.biojava.bio.program.blast2html.BlastLikeAlignment is defined
in Blast2HTMLHandler.java.
Because it is used outside of its source file, it should be defined in a
file called
"BlastLikeAlignment.java".
[javac] void writeCurrentHSP( HSPSummary oHSPSummary,
BlastLikeAlignment oAlignment ) {
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/program/blast2html/HTMLRenderer.java:543:
class org.biojava.bio.program.blast2html.HSPSummary is defined in
Blast2HTMLHandler.java. Because it is
used outside of its source file, it should be defined in a file called
"HSPSummary.java".
[javac] void writeCurrentHSP( HSPSummary oHSPSummary,
BlastLikeAlignment oAlignment ) {
[javac] ^
[javac]
HOME/JAVA/biojava-live/ant-build/src/main/org/biojava/bio/gui/sequence/PairwiseFilteringRenderer.java:436:
No method matching hasListeners() found in class
org.biojava.bio.gui.sequence.PairwiseFilteringRenderer.
[javac] if (hasListeners())
[javac] ^
[javac] Note: 2 files use or override a deprecated API. Recompile
with "-deprecation" for details.
[javac] 6 errors, 5 warnings
BUILD FAILED
HOME/JAVA/biojava-live/build.xml:140: Compile failed, messages should
have been provided.
Total time: 3 minutes 5 seconds
_______________________________________________
Biojava-l mailing list - [EMAIL PROTECTED]
http://biojava.org/mailman/listinfo/biojava-l
