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From Michael Baessler <...@michael-baessler.de>
Subject Re: bioNLP question
Date Wed, 11 Jun 2008 07:55:03 GMT
Hi Ahmed,

I think you should post your question to the users list, since the issue are not directly
related to
the UIMA framework. On the uima-users list you will have a bigger audience
of UIMA users that may have experiences with that and possibly can help you with that.

http://incubator.apache.org/uima/mail-lists.html

-- Michael

Ahmed Abdeen(Home) wrote:
> Hello,Apologies for crosslisting!
> I am building the bioNLP project but I am getting compilation issues with
> biotagger.jar and stanford-parser.jar files. They both seem to be outdates
> because some classes/methods are missing. I included the jars in the lib
> directory after downloading them from the places pointed in the readme file
> in the bioNLP distribution. Following are the errors that I am getting when
> using ant. I would appreciate any help on that:
> 
> Buildfile: build.xml
> 
> clean:
>    [delete] Deleting directory
> /Users/ahmedabdeen/Projects/bionlp_uima_repository-1.0.1/build
> 
> compile:
>     [mkdir] Created dir:
> /Users/ahmedabdeenhamed/Projects/bionlp_uima_repository-1.0.1/build
>     [mkdir] Created dir:
> /Users/ahmedabdeenhamed/Projects/bionlp_uima_repository-1.0.1/build/classes
>     [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
> /Users/ahmedabdeenhamed/Projects/bionlp_uima_repository-1.0.1/ant/build.xml:61:
> Compile failed; see the compiler error output for details.
> 
> Thanks in advance!
> Ahmed
> 


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