ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Wu, Stephen T., Ph.D." <Wu.Step...@mayo.edu>
Subject Re: Errors from cleartk?
Date Wed, 31 Jul 2013 16:16:47 GMT
Well, the errors I see in eclipse are about failures to import cleartk
classes.  

The "correspond pretty well" between eclipse errors and maven warnings
might be bogus... I was just extrapolating from the fact that some of the
same projects (ctakes-assertion, ctakes-temporal) are unable to build
correctly + have maven warnings.  ctakes-distribution has maven warnings
only, and ctakes-relation-extractor has eclipse errors only.

stephen




On 7/31/13 10:57 AM, "Steven Bethard" <steven.bethard@Colorado.EDU> wrote:

>On 31 Jul2013, at 8:17 , "Wu, Stephen T., Ph.D." <Wu.Stephen@mayo.edu>
>wrote:
>> 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.
>
>By the way, I'm still a little confused because your subject says "Errors
>from cleartk?" but none of the warnings below say anything about ClearTK.
>
>Steve
>
>
>>  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>
>>> 
>> 
>

Mime
View raw message