[Biojava-dev] build failure strangeness: bogus errors

[Thomas Down]

I think Sylvain's error was caused by having an existing biojava.jar
on his CLASSPATH (or maybe in the lib/ext directory).  Have you checked
for that?

    Thomas.

Once upon a time, Keith James wrote:
> 
> I've got build failures on a fresh checkout since the projection
> changes (identical to Sylvian's):
> 
> compile:
>     [javac] Compiling 1069 source files to /nfs/team81/kdj/dev/biojava-live/ant-build
> /classes/main
>     [javac] /nfs/team81/kdj/dev/biojava-live/ant-build/src/main/org/biojava/bio/seq/i
> mpl/RevCompSequence.java:47: reference to ProjectedFeatureHolder is ambiguous, both c
> lass org.biojava.bio.seq.projection.ProjectedFeatureHolder in org.biojava.bio.seq.pro
> jection and class org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq m
> atch
>     [javac]     private ProjectedFeatureHolder pfh;
>     [javac]             ^
>     [javac] /nfs/team81/kdj/dev/biojava-live/ant-build/src/main/org/biojava/bio/seq/i
> mpl/RevCompSequence.java:63: reference to ProjectedFeatureHolder is ambiguous, both c
> lass org.biojava.bio.seq.projection.ProjectedFeatureHolder in org.biojava.bio.seq.pro
> jection and class org.biojava.bio.seq.ProjectedFeatureHolder in org.biojava.bio.seq m
> atch
>     [javac]         pfh = new ProjectedFeatureHolder(new TranslateFlipContext(seq,thi
> s,seq.length()+1,true));
>     [javac]                   ^
>     [javac] /nfs/team81/kdj/dev/biojava-live/ant-build/src/main/org/biojava/bio/seq/S
> equenceTools.java:90: cannot resolve symbol
>     [javac] symbol  : constructor SubSequence (org.biojava.bio.seq.Sequence,int,int,j
> ava.lang.String)
>     [javac] location: class org.biojava.bio.seq.SubSequence
>     [javac]     return new SubSequence(seq, start, end, name);
>     [javac]            ^
>     [javac] 3 errors