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From Marshall Schor <...@schor.com>
Subject Re: bioNLP UIMA
Date Wed, 11 Jun 2008 19:23:02 GMT
Hello, Ahmed -

I think this question is best directed to the bioNLP group. 

It looks like the build script is not finding many different classes.  
Perhaps there is a "readme" in the distribution you got which gives 
instructions on obtaining other Jars from places like Stanford (the 
import of "edu.stanford.nlp. . ." implies this may be coming from 
Standford university).

-Marshall

Ahmed Abdeen(Home) wrote:
> Apologies from cross-listing!
>
> Hello,I am trying to compile bioNLP UIMA tools but I am getting the
> following errors:
> Buildfile: build.xml
>
> compile:
>     [javac] Compiling 161 source files to
> /Users/ahmedabdeenhamed/Projects/bionlp_uima_repository-1.0.1/build/classes
>     [javac]
> /Users/ahmedabdeenhamed/Projects/bionlp_uima_repository-1.0.1/src/edu/uchsc/ccp/util/external/stanfordparser/StanfordParser_Util.java:48:
> cannot find symbol
>     [javac] symbol  : class TypedDependencyList
>     [javac] location: package edu.stanford.nlp.trees
>     [javac] import edu.stanford.nlp.trees.TypedDependencyList;
>     [javac]                               ^
>     [javac]
> /Users/ahmedabdeenhamed/Projects/bionlp_uima_repository-1.0.1/src/edu/uchsc/ccp/util/external/stanfordparser/StanfordParser_Util.java:418:
> cannot find symbol
>     [javac] symbol  : class TypedDependencyList
>     [javac] location: class
> edu.uchsc.ccp.util.external.stanfordparser.StanfordParser_Util
>     [javac]         TypedDependencyList tdl = gs.typedDependencies();
>     [javac]         ^
>     [javac]
> /Users/ahmedabdeenhamed/Projects/bionlp_uima_repository-1.0.1/src/edu/uchsc/ccp/util/external/penn/PennBioTokenizer_Util.java:49:
> cannot find symbol
>     [javac] symbol  : constructor BioTokenizer(java.lang.String)
>     [javac] location: class edu.upenn.cis.tokenizers.BioTokenizer
>     [javac]         bt = new BioTokenizer(tokenizerModelFile);
>     [javac]              ^
>     [javac] Note: Some input files use or override a deprecated API.
>     [javac] Note: Recompile with -Xlint:deprecation for details.
>     [javac] Note: Some input files use unchecked or unsafe operations.
>     [javac] Note: Recompile with -Xlint:unchecked for details.
>     [javac] 3 errors
>
> BUILD FAILED
>
> If you have had experience with bioNLP UIMA and got it to compile, please
> let me know. I could use some help.
> Thanks in advance!
> Ahmed
>
>   


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