[Biojava-l] Build failing

[Brian Gilman]

Wow,

	I'm very excited to hear Matthew endorse web services as a
potential direction for the hackathon. As you already know, I've been
tauting/using/running our department off a web services architecture for
three years now. I'd love help to web services enable Bio-Java for the
rest of the world to use! 

	This is right in line for the goals of the OmniGene project,
MOBY, and openBQS. Correct me if I'm wrong Mark and Martin but, I think
there might be some wonderful opportunities to start webservicesifying the
biojava framework. 

	I guess this is a HUGE hand in the air as a volunteer on that
project. I've also got a lot of experience writing web services in Perl,
Python, C++,C# and javascript (mozilla API). So, bombard me with
questions!! I'm not sure I'll be able to answer all of them but, I'll try
:)  

				Best, 

					-B

-----------------------
Brian Gilman <gilmanb@genome.wi.mit.edu>
Group Leader Medical & Population Genetics Dept.
MIT/Whitehead Inst. Center for Genome Research
One Kendall Square, Bldg. 300 / Cambridge, MA 02139-1561 USA
phone +1 617  252 1069 / fax +1 617 252 1902


On Wed, 11 Dec 2002, Matthew Pocock wrote:

> Hi David,
> 
> Is it possible that you have either a truncated or corrupted version of 
> the biojava source tree? I'm sure we've broken the 1k mark for source 
> files now. We're getting better at hiding them away though ;-)
> 
> Try checking the files out again from clean. That may sort things out.
> 
> Matthew
> 
> David Waring wrote:
> > I got the following errors when I tried to build biojava-live
> > 
> > compile:
> >     [javac] Compiling 799 source files to
> > V:\dwaring\cvs\biojava-live\ant-build\
> > classes\main
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:198: interface expected here
> >     [javac]     private static class BlankFilterWriter implements
> > XMLFilterWrite
> > r {
> >     [javac]                                                       ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:217: interface expected here
> >     [javac]     private static abstract class PropertyFilterWriter
> > implements XM
> > LFilterWriter {
> >     [javac]
> > ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:313: interface expected here
> >     [javac]     private static class AndFilterWriter implements
> > XMLFilterWriter
> > {
> >     [javac]                                                     ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:340: interface expected here
> >     [javac]     private static class OrFilterWriter implements
> > XMLFilterWriter {
> > 
> >     [javac]                                                    ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:112: cannot resolve symbol
> >     [javac] symbol  : class IsTopLevel
> >     [javac] location: interface org.biojava.bio.seq.FeatureFilter
> >     [javac]                 FeatureFilter.IsTopLevel.class,
> >     [javac]                              ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\seq\i
> > o\filterxml\XMLFilterWriterConfig.java:185:
> > writeFilter(org.biojava.bio.seq.Feat
> > ureFilter,org.biojava.utils.xml.XMLWriter) in
> > org.biojava.bio.seq.io.filterxml.X
> > MLFilterWriter cannot be applied to
> > (org.biojava.bio.seq.FeatureFilter,org.bioja
> > va.utils.xml.XMLWriter,org.biojava.bio.seq.io.filterxml.XMLFilterWriterConfi
> > g)
> >     [javac]                 xfw.writeFilter(ff, xw, this);
> >     [javac]                    ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
> > am\das\DASMergeFeatureHolder.java:35: cannot resolve symbol
> >     [javac] symbol  : method getMergeMap  ()
> >     [javac] location: class
> > org.biojava.bio.program.das.DASMergeFeatureHolder
> >     [javac]     Map mm = getMergeMap();
> >     [javac]                  ^
> >     [javac]
> > V:\dwaring\cvs\biojava-live\ant-build\src\main\org\biojava\bio\progr
> > am\das\DASMergeFeatureHolder.java:48: cannot resolve symbol
> >     [javac] symbol  : method getMergeMap  ()
> >     [javac] location: class
> > org.biojava.bio.program.das.DASMergeFeatureHolder
> >     [javac]     Map mm = getMergeMap();
> >     [javac]                  ^
> >     [javac] Note: Some input files use or override a deprecated API.
> >     [javac] Note: Recompile with -deprecation for details.
> >     [javac] 8 errors
> > 
> > BUILD FAILED
> > file:V:/dwaring/cvs/biojava-live/build.xml:281: Compile failed; see the
> > compiler
> >  error output for details.
> > 
> > Total time: 1 minute 27 seconds
> > 
> > 
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> 
> 
> -- 
> BioJava Consulting LTD - Support and training for BioJava
> http://www.biojava.co.uk
> 
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