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Posted to user@uima.apache.org by "Ahmed Abdeen(Home)" <ah...@gmail.com> on 2008/06/11 17:01:11 UTC
bioNLP UIMA
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
Re: bioNLP UIMA
Posted by "Ahmed Abdeen(Home)" <ah...@gmail.com>.
Dear Marshall,
Thank you for your research, I appreciate it. I ended up removing references
to the missing files from the source code and I got it to compile.Best
wishes,
Ahmed
On Wed, Jun 11, 2008 at 6:09 PM, Marshall Schor <ms...@schor.com> wrote:
> Ahmed Abdeen(Home) wrote:
>
>> Hi Marshall,I actually sent my question there and I was told that those
>> files aren't there's to begin with. I was advised to check with uima-users
>> after I posted my question to the uima-developers list.
>>
>>
> I think you would get these files from the universities mentioned. For
> instance, for some of the missing files below, they have names like
> Standford Parser, and there is a parser available for download from
> http://nlp.stanford.edu/software/lex-parser.shtml which might be that
> parser.
> -Marshall
>
> Thanks for your response anyways!
>> Ahmed
>>
>> On Wed, Jun 11, 2008 at 3:23 PM, Marshall Schor <ms...@schor.com> wrote:
>>
>>
>>
>>> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>
>
Re: bioNLP UIMA
Posted by Marshall Schor <ms...@schor.com>.
Ahmed Abdeen(Home) wrote:
> Hi Marshall,I actually sent my question there and I was told that those
> files aren't there's to begin with. I was advised to check with uima-users
> after I posted my question to the uima-developers list.
>
I think you would get these files from the universities mentioned. For
instance, for some of the missing files below, they have names like
Standford Parser, and there is a parser available for download from
http://nlp.stanford.edu/software/lex-parser.shtml which might be that
parser.
-Marshall
> Thanks for your response anyways!
> Ahmed
>
> On Wed, Jun 11, 2008 at 3:23 PM, Marshall Schor <ms...@schor.com> wrote:
>
>
>> 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
>>>
>>>
>>>
>>>
>>
>
>
Re: bioNLP UIMA
Posted by "Ahmed Abdeen(Home)" <ah...@gmail.com>.
Hi Marshall,I actually sent my question there and I was told that those
files aren't there's to begin with. I was advised to check with uima-users
after I posted my question to the uima-developers list.
Thanks for your response anyways!
Ahmed
On Wed, Jun 11, 2008 at 3:23 PM, Marshall Schor <ms...@schor.com> wrote:
> 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
>>
>>
>>
>
>
Re: bioNLP UIMA
Posted by Marshall Schor <ms...@schor.com>.
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
>
>