[Biojava-l] Problems building from CVS sources

[Mark Schreiber]

Hi, 

What JAVAC are you using, I seem to be able to build this fine.

Mark

On Mon, 29 Oct 2001, Howard Ungar wrote:

> 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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> 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Mark Schreiber			Ph: 64 3 4797875
Rm 218				email mark_s@sanger.otago.ac.nz
Department of Biochemistry	email m.schreiber@clear.net.nz
University of Otago		
PO Box 56
Dunedin
New Zealand
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~