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From "Wu, Stephen T., Ph.D." <Wu.Step...@mayo.edu>
Subject Re: Errors from cleartk?
Date Wed, 31 Jul 2013 14:17:55 GMT
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...?

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 don┬╣t 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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