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From Steven Bethard <steven.beth...@Colorado.EDU>
Subject Re: Errors from cleartk?
Date Wed, 31 Jul 2013 15:55:37 GMT
On 31 Jul2013, at 8:17 , "Wu, Stephen T., Ph.D." <Wu.Stephen@mayo.edu> wrote:
> Yeah I tried the typical eclipse tricks.
> 
> The warnings from mvn compile do correspond pretty well to the errors that
> eclipse shows, though. In case the attachment wasn't clear, I've included
> the warnings below.  I just don't know what to do about them…?

I see. So your Eclipse is failing on warnings, not just on errors? And Maven -> Update
Project didn't work...

I wonder if there's something wrong with your m2e plugin. Maybe try uninstalling and reinstalling
it?

Steve

> 
> stephen
> 
> 
> [WARNING] Some problems were encountered while building the effective
> model for org.apache.ctakes:ctakes-assertion:jar:3.1.0-SNAPSHOT
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)'
> must be unique: junit:junit:jar -> duplicate declaration of version (?) @
> line 154, column 15
> [WARNING] 'dependencies.dependency.systemPath' for
> org.mitre.medfacts:medfacts-i2b2:jar should not point at files within the
> project directory, ${project.basedir}/lib/med-facts-i2b2-1.2-SNAPSHOT.jar
> will be unresolvable by dependent projects @ line 192, column 16
> [WARNING] 'dependencies.dependency.systemPath' for
> org.mitre.medfacts:medfacts-zoner:jar should not point at files within the
> project directory, ${project.basedir}/lib/med-facts-zoner-1.1.jar will be
> unresolvable by dependent projects @ line 199, column 16
> [WARNING] 'dependencies.dependency.systemPath' for
> org.mitre.jcarafe.core:jcarafe.core:jar should not point at files within
> the project directory,
> ${project.basedir}/lib/jcarafe-core_2.9.1-0.9.8.3.RC4.jar will be
> unresolvable by dependent projects @ line 206, column 16
> [WARNING] 'dependencies.dependency.systemPath' for
> org.mitre.jcarafe.ext:jcarafe.ext:jar should not point at files within the
> project directory, 
> ${project.basedir}/lib/jcarafe-ext_2.9.1-0.9.8.3.RC4.jar will be
> unresolvable by dependent projects @ line 213, column 16
> [WARNING] 
> [WARNING] Some problems were encountered while building the effective
> model for org.apache.ctakes:ctakes-temporal:jar:3.1.0-SNAPSHOT
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)'
> must be unique: org.jdom:jdom2:jar -> duplicate declaration of version (?)
> @ line 91, column 17
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)'
> must be unique: com.lexicalscope.jewelcli:jewelcli:jar -> duplicate
> declaration of version (?) @ line 95, column 21
> [WARNING] 
> [WARNING] Some problems were encountered while building the effective
> model for org.apache.ctakes:ctakes-distribution:pom:3.1.0-SNAPSHOT
> [WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)'
> must be unique: org.apache.ctakes:ctakes-ne-contexts:jar -> duplicate
> declaration of version (?) @ line 99, column 15
> [WARNING] 
> [WARNING] It is highly recommended to fix these problems because they
> threaten the stability of your build.
> [WARNING] 
> [WARNING] For this reason, future Maven versions might no longer support
> building such malformed projects.
> 
> 
> 
> 
> 
> 
> On 7/31/13 8:50 AM, "Steven Bethard" <steven.bethard@Colorado.EDU> wrote:
> 
>> On 31 Jul2013, at 7:12 , "Wu, Stephen T., Ph.D." <Wu.Stephen@mayo.edu>
>> wrote:
>>> Steve, warnings from mvn compile are attached.  Afterwards, mvn compile
>>> finished successfully with no other warnings or errors.
>> 
>> So if `mvn compile` doesn't give any errors, I guess the errors you're
>> seeing are in Eclipse? Have you tried the usual tricks to get Eclipse to
>> refresh? Here are 4 of the things I try when Eclipse is acting up:
>> 
>> * Go to Project -> Clean, select Clean all projects and hit Ok
>> * Right click the project, then go to Refresh to sync up with the local
>> filesystem
>> * Right click, then go to Maven2 -> Update Project
>> * Close and Open Project
>> 
>> Steve
>> 
>>> 
>>> Pei, I've definitely compiled this particular environment successfully
>>> after the clear-tk lib upgrades.  Poms, etc, are showing that they are
>>> updated correctly. I've tried maven updates, svn updates, clean &
>>> rebuild,
>>> refreshes, etcs multiple times in eclipse.
>>> 
>>> I don¹t think it's a general problem because I have other environments
>>> doing just fine, and Jenkins is not showing problems.
>>> 
>>> Thanks!
>>> 
>>> stephen
>>> 
>>> 
>>> On 7/30/13 6:38 PM, "Steven Bethard" <steven.bethard@Colorado.EDU>
>>> wrote:
>>> 
>>>> On 30 Jul2013, at 7:32 , "Wu, Stephen T., Ph.D." <Wu.Stephen@mayo.edu>
>>>> wrote:
>>>>> Is anyone else getting errors importing from cleartk?  In one of my
>>>>> environments,  the following projects:
>>>>> ctakes-assertion
>>>>> ctakes-relation-extractor
>>>>> ctakes-temporal
>>>>> are complaining about not finding these classes
>>>>> - org.cleartk.classifier.liblinear.LIBLINEARStringOutcomeDataWriter
>>>>> - org.cleartk.classifier.tksvmlight.model
>>>>> 
>>>>> Did I somehow lose the cleartk-ml stuff?  Afaik all of this was
>>>>> running
>>>>> before... I have not modified any maven dependenciesŠ
>>>> 
>>>> Could you paste the output of `mvn compile`?
>>>> 
>>>> Steve
>>> 
>>> <mvn_compile_output.txt>
>> 
> 


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