[Biojava-l] Problems building from CVS sources

[Howard Ungar]

I am having problems compling 4 of the files in the CVS archives.  I
was trying to get the latest version of certain other files when I ran
into this.

C:\java\biojava-live>ant
Searching for build.xml ...
Buildfile: C:\java\biojava-live\build.xml

init:

prepare:

prepare-src:

compile:
    [javac] Compiling 4 source files to
C:\java\biojava-live\ant-build\classes\m
ain
    [javac] Modern compiler is not available - using classic compiler
    [javac]
C:\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]
C:\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 can
not 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]
C:\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 cann
ot 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]
C:\java\biojava-live\ant-build\src\main\org\biojava\bio\seq\db\emblcd\EmblCDROMRandomAccess.java:84:
Exception java.io.IOException must be caught, or it must be declared in
the throws clause of this constructor.
    [javac]         raIndexFile = new RandomAccessFile(indexFile, "r");
    [javac]                       ^
    [javac]
C:\java\biojava-live\ant-build\src\main\org\biojava\bio\seq\Projecte
dFeatureHolder.java:57: Blank final variable 'wrapped' may not have
been initialized. It must be assigned a value in an initializer, or in
every constructor.
    [javac]     private final FeatureHolder wrapped;
    [javac]                                        ^
    [javac]
C:\java\biojava-live\ant-build\src\main\org\biojava\bio\seq\ProjectedFeatureHolder.java:58:
Blank final variable 'parent' may not have been initialized. It must be
assigned a value in an initializer, or in every constructor.
    [javac]     private final FeatureHolder parent;
    [javac]                                       ^
    [javac]
C:\java\biojava-live\ant-build\src\main\org\biojava\bio\seq\ProjectedFeatureHolder.java:59:
Blank final variable 'translate' may not have been initialized. It must
be assigned a value in an initializer, or in every constructor.
    [javac]     private final int translate;
    [javac]                                ^
    [javac] Note:
C:\java\biojava-live\ant-build\src\main\org\biojava\bio\seq\ProjectedFeatureHolder.java
uses or overrides a deprecated API.  Recompile with "-deprecation" for
details.
    [javac] 7 errors, 1 warning

BUILD FAILED

--- Keith James <kdj@sanger.ac.uk> wrote:
> 
> Instead I have added support for the QueryId and DatabaseId elements
> described in the DTD and the BlastSAXParser now emits these elements
> for Blast (but not HMMER).
> 

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