[Biojava-l] ant javadoc succeeds but ant package fails!

[Geetha Vasudevan]

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