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From Don Flinn <fl...@alum.mit.edu>
Subject Re: Errors in Install and examples [EXTERNAL]
Date Mon, 22 Jan 2018 16:02:50 GMT
Hi Sean,

Thank you for the information.  I'm looking through the examples and other
code.  CTAKES is surely an impressive work.

Don

On Mon, Jan 22, 2018 at 9:55 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Don,
>
> To run the standard ctakes clinical pipeline you don't need the ytex
> module, so indeed do not panic.  If you are not getting a proper build
> because of ytex then my advice (without analyzing that output) would be to
> just comment out the dependency in the main ctakes pom.  If you ever do
> decide to play with ytex then you can tackle any build problems at that
> time.
>
> Don't use the MultiThreadedPipeline in ctakes examples.  I am 99% sure
> that it doesn't work (I've run it, gotten errors, and then hunted through
> the code until I found unprotected shared objects.)  If you do want to try
> a thread safe pipeline then I recommend that you get the trunk version of
> ctakes.  With that you can build using the "runPiperSubmitter" maven
> profile to launch a gui.  In the gui select the "TsFastClinicalPipeline"
> (or something like that) in ctakes-clinical-pipeline-res.  "Ts" stands for
> thread-safe and you can find Ts piper files throughout the ctakes *-res
> projects.
>
> You can check progress /comments at this jira item (ctakes-485):
> https://issues.apache.org/jira/browse/CTAKES-485?jql=
> project%20%3D%20CTAKES%20ORDER%20BY%20created%20DESC
>
> Sean
> ________________________________________
> From: Don Flinn <flinn@alum.mit.edu>
> Sent: Sunday, January 21, 2018 9:41 PM
> To: dev@ctakes.apache.org
> Subject: Errors in Install and examples [EXTERNAL]
>
> Hi,
>
> I'm new toctakes.  I installed the system as per the cTakes 4.0 Developer
> install Guide into eclipse running on Windows 10.  It mostly went well.
> However, there were errors in the build for the ctakes-ytexs in the pom.xml
> <execution> elements.  It said 'don't panic" so I'm not -:).  However, due
> my novice status, I don't know how to fix this.  The error message is
> below.  Some ideas would be appreciated
>
> I also ran through the examples and MultiTheadedPipeline.java had an error
> shown below:  I would appreciate any insight into these errors.
>
> I still have a lot of work to do to understand all the output and
> processes, but I want to first get the install correct.  I've been reading
> the ctakes, UMIA and NPL documents and articles.  I would appreciate any
> pointers to pertinent references that I should read.
>
> Thanks,
> Don
>
> ========================================Build error
> ==============================
>
> An Ant BuildException has occured: The following error occurred while
> executing this line: C:\apache-ctakes-4.0.0Dev\ctakes\ctakes-
>  ytex\scripts\build-setup.xml:113: Problem: failed to create task or type
> if Cause: the class net.sf.antcontrib.logic.IfTask was not found. Action:
>  Check that the component has been correctly declared and that the
> implementing JAR is in one of: -ANT_HOME\lib -the IDE Ant configuration
>  dialogs Do not panic, this is a common problem. It may just be a
> typographical error in the build file or the task/type declaration. The
> commonest
>  cause is a missing JAR. This is not a bug; it is a configuration problem
> (org.apache.maven.plugins:maven-antrun-plugin:1.6:run:generate-test-
>  config:pre-integration-test) org.apache.maven.plugin.
> MojoExecutionException:
> An Ant BuildException has occured: The following error occurred
>  while executing this line: C:\apache-ctakes-4.0.0Dev\
> ctakes\ctakes-ytex\scripts\build-setup.xml:113: Problem: failed to create
> task or type if Cause:
>  the class net.sf.antcontrib.logic.IfTask was not found. Action: Check that
> the component has been correctly declared and that the implementing
>  JAR is in one of: -ANT_HOME\lib -the IDE Ant configuration dialogs Do not
> panic, this is a common problem. It may just be a typographical error
>  in the build file or the task/type declaration. The commonest cause is a
> missing JAR. This is not a bug; it is a configuration problem at
>  org.apache.maven.plugin.antrun.AntRunMojo.execute(AntRunMojo.java:283) at
>  org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(
> DefaultBuildPluginManager.java:134) at
>  org.eclipse.m2e.core.internal.embedder.MavenImpl.execute(
> MavenImpl.java:331)
> at
>  org.eclipse.m2e.core.internal.embedder.MavenImpl$11.call(
> MavenImpl.java:1362)
> at
>  org.eclipse.m2e.core.internal.embedder.MavenImpl$11.call(
> MavenImpl.java:1)
> at
>  org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare(
> MavenExecutionContext.java:177) at
>  org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute(
> MavenExecutionContext.java:112) at
>  org.eclipse.m2e.core.internal.embedder.MavenImpl.execute(
> MavenImpl.java:1360)
> at
>  org.eclipse.m2e.core.project.configurator.MojoExecutionBuildParticipant.
> build(MojoExecutionBuildParticipant.java:52) at
>  org.eclipse.m2e.core.internal.builder.MavenBuilderImpl.
> build(MavenBuilderImpl.java:137)
> at
>  org.eclipse.m2e.core.internal.builder.MavenBuilder$
> 1.method(MavenBuilder.java:172) at
>  org.eclipse.m2e.core.internal.builder.MavenBuilder$1.method(
> MavenBuilder.java:1)
> at
>  org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod$1$1.call(
> MavenBuilder.java:115)
> at
>  org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare(
> MavenExecutionContext.java:177) at
>  org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute(
> MavenExecutionContext.java:112) at
>  org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod$1.call(
> MavenBuilder.java:105)
> at
>  org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare(
> MavenExecutionContext.java:177) at
>  org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute(
> MavenExecutionContext.java:151) at
>  org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute(
> MavenExecutionContext.java:99)
> at
>  org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod.execute(
> MavenBuilder.java:86)
> at
>  org.eclipse.m2e.core.internal.builder.MavenBuilder.build(
> MavenBuilder.java:200)
> at
>  org.eclipse.core.internal.events.BuildManager$2.run(
> BuildManager.java:735)
> at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42) at
>  org.eclipse.core.internal.events.BuildManager.
> basicBuild(BuildManager.java:206)
> at
>  org.eclipse.core.internal.events.BuildManager.
> basicBuild(BuildManager.java:246)
> at
>  org.eclipse.core.internal.events.BuildManager$1.run(
> BuildManager.java:301)
> at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42) at
>  org.eclipse.core.internal.events.BuildManager.
> basicBuild(BuildManager.java:304)
> at
>  org.eclipse.core.internal.events.BuildManager.
> basicBuildLoop(BuildManager.java:360)
> at
>  org.eclipse.core.internal.events.BuildManager.build(
> BuildManager.java:383)
> at
>  org.eclipse.core.internal.events.AutoBuildJob.doBuild(
> AutoBuildJob.java:142)
> at
>  org.eclipse.core.internal.events.AutoBuildJob.run(AutoBuildJob.java:232)
> at org.eclipse.core.internal.jobs.Worker.run(Worker.java:56) Caused by: C:
>  \apache-ctakes-4.0.0Dev\ctakes\ctakes-ytex\target\
> antrun\build-main.xml:5:
> The following error occurred while executing this line: C:\apache-
>  ctakes-4.0.0Dev\ctakes\ctakes-ytex\scripts\build-setup.xml:113: Problem:
> failed to create task or type if Cause: the class
>  net.sf.antcontrib.logic.IfTask was not found. Action: Check that the
> component has been correctly declared and that the implementing JAR is in
>  one of: -ANT_HOME\lib -the IDE Ant configuration dialogs Do not panic,
> this is a common problem. It may just be a typographical error in the
>  build file or the task/type declaration. The commonest cause is a missing
> JAR. This is not a bug; it is a configuration problem at
>  org.apache.tools.ant.ProjectHelper.addLocationToBuildException(
> ProjectHelper.java:497)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:
>  444) at org.apache.tools.ant.UnknownElement.execute(
> UnknownElement.java:291)
> at sun.reflect.GeneratedMethodAccessor152.invoke(Unknown
>  Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown
> Source)
> at java.lang.reflect.Method.invoke(Unknown Source) at
>  org.apache.tools.ant.dispatch.DispatchUtils.execute(
> DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348) at
>  org.apache.tools.ant.Target.execute(Target.java:390) at
> org.apache.tools.ant.Target.performTasks(Target.java:411) at
>  org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397) at
> org.apache.tools.ant.Project.executeTarget(Project.java:1366) at
>  org.apache.maven.plugin.antrun.AntRunMojo.execute(AntRunMojo.java:270)
> ...
> 32 more Caused by: C:\apache-ctakes-4.0.0Dev\ctakes\ctakes-
>  ytex\scripts\build-setup.xml:113: Problem: failed to create task or type
> if Cause: the class net.sf.antcontrib.logic.IfTask was not found. Action:
>  Check that the component has been correctly declared and that the
> implementing JAR is in one of: -ANT_HOME\lib -the IDE Ant configuration
>  dialogs Do not panic, this is a common problem. It may just be a
> typographical error in the build file or the task/type declaration. The
> commonest
>  cause is a missing JAR. This is not a bug; it is a configuration problem
> at
>  org.apache.tools.ant.UnknownElement.getNotFoundException(
> UnknownElement.java:487)
> at
>  org.apache.tools.ant.UnknownElement.makeObject(UnknownElement.java:419)
> at
>  org.apache.tools.ant.UnknownElement.maybeConfigure(
> UnknownElement.java:163)
> at org.apache.tools.ant.Task.perform(Task.java:347) at
>  org.apache.tools.ant.Target.execute(Target.java:390) at
> org.apache.tools.ant.Target.performTasks(Target.java:411) at
>  org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397) at
>  org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(
> SingleCheckExecutor.java:38)
> at
>  org.apache.tools.ant.Project.executeTargets(Project.java:1249) at
> org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442) ... 43 more
>
> ===================== MultiTheadedPipeline.java
> error===================================
> ** Configuration Error: file:\C:\apache-ctakes-4.0.
> 0Dev\ctakes\ctakes-lvg-res\target\classes\org\apache\
> ctakes\lvg\data\config\lvg.properties (The filename, directory name, or
> volume label syntax is incorrect)
> ** Error: problem of opening/reading config file:
> 'file:\C:\apache-ctakes-4.0.0Dev\ctakes\ctakes-lvg-res\
> target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x
> option to specify the config file path.
> ** Configuration Error: file:\C:\apache-ctakes-4.0.
> 0Dev\ctakes\ctakes-lvg-res\target\classes\org\apache\
> ctakes\lvg\data\config\lvg.properties (The filename, directory name, or
> volume label syntax is incorrect)
> ** Error: problem of opening/reading config file:
> 'file:\C:\apache-ctakes-4.0.0Dev\ctakes\ctakes-lvg-res\
> target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x
> option to specify the config file path.
>

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