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Posted to dev@ctakes.apache.org by Karthik Sarma <ks...@ksarma.com> on 2013/01/09 01:30:14 UTC
Failure on unpack-dependencies?
Hi folks,
I was trying to get the trunk up and running on a new windows 8 machine
(completely clean). Installed jdk, eclipse (classic/juno), m2e, and
subversive. I used eclipse's import feature with maven from SCM. Checkout
was fine, but ctakes-dictionary-lookup was not able to build (as far as I
could tell, everything else built just fine. Here is the error:
Execution unpack-dependencies of goal
org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-dependencies
failed: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.6 or one
of its dependencies could not be resolved: Failed to collect dependencies
for org.apache.maven.plugins:maven-dependency-plugin:jar:2.6 ()
(org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-dependencies:unpack-dependencies:process-resources)
pom.xml /ctakes-dictionary-lookup line 82
I did a few checks to try to diagnose the issue -- the pom seems to be
correct, and the m2e fix for unpack also seems to be correct. The plugin
itself (for umls) exists in my local repository, as does
maven-dependency-plugin 2.6. There aren't any spaces or other oddities in
any of the paths. I tried cleaning, re-acquiring the source, and even
deleting eclipse and starting from scratch, but alas, no dice.
Is anyone else having a similar issue? Jenkins says everything should be
working fine. I should probably just try building without involving eclipse
at all, which I will do next.
Karthik
--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical
Association
ksarma@ksarma.com
gchat: ksarma@gmail.com
linkedin: www.linkedin.com/in/ksarma
RE: Failure on unpack-dependencies?
Posted by "Masanz, James J." <Ma...@mayo.edu>.
I will be checking out from trunk this afternoon into eclipe (Juno/classic) with m2e 1.2.0 and will report back
- James Masanz
> -----Original Message-----
> From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of Karthik
> Sarma
> Sent: Tuesday, January 08, 2013 6:30 PM
> To: cTAKES Developer List
> Subject: Failure on unpack-dependencies?
>
> Hi folks,
>
> I was trying to get the trunk up and running on a new windows 8 machine
> (completely clean). Installed jdk, eclipse (classic/juno), m2e, and
> subversive. I used eclipse's import feature with maven from SCM. Checkout
> was fine, but ctakes-dictionary-lookup was not able to build (as far as I
> could tell, everything else built just fine. Here is the error:
>
> Execution unpack-dependencies of goal
> org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-dependencies
> failed: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.6 or one
> of its dependencies could not be resolved: Failed to collect dependencies
> for org.apache.maven.plugins:maven-dependency-plugin:jar:2.6 ()
> (org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-
> dependencies:unpack-dependencies:process-resources)
> pom.xml /ctakes-dictionary-lookup line 82
>
> I did a few checks to try to diagnose the issue -- the pom seems to be
> correct, and the m2e fix for unpack also seems to be correct. The plugin
> itself (for umls) exists in my local repository, as does maven-dependency-
> plugin 2.6. There aren't any spaces or other oddities in any of the paths.
> I tried cleaning, re-acquiring the source, and even deleting eclipse and
> starting from scratch, but alas, no dice.
>
> Is anyone else having a similar issue? Jenkins says everything should be
> working fine. I should probably just try building without involving
> eclipse at all, which I will do next.
>
>
> Karthik
>
>
> --
> Karthik Sarma
> UCLA Medical Scientist Training Program Class of 20??
> Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to
> the House of Delegates of the American Medical Association
> ksarma@ksarma.com
> gchat: ksarma@gmail.com
> linkedin: www.linkedin.com/in/ksarma
RE: Failure on unpack-dependencies? [ctakes-dictionary-lookup
problem with rxnorm_index]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Yes, it is the Lucene problem re: reading from a jar. Get rid of that jar from your lib/ and make certain that your dictionary/lookup/ looks good.
Btw, this is Jira CTAKES-121
-----Original Message-----
From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
Sent: Friday, January 18, 2013 1:46 PM
To: <ct...@incubator.apache.org>
Cc: ctakes-dev@incubator.apache.org
Subject: Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup problem with rxnorm_index]
I wonder if its worth it to update the instructions to just unzip it manually. Probably more complicated to try to do it automatically do it with the plugins...
Or remove the requirement to unpack jars (I think it was a Lucene limitation not be able to read from a jar file)
Sent from my iPhone
On Jan 18, 2013, at 1:32 PM, "Coarr, Matt" <mc...@mitre.org> wrote:
> Tim, did you ever manage to get this working? Does anyone else have any ideas on this problem?
>
> I'm trying to run the full pipeline on the ctakes trunk and I'm running into the same issue - rxnorm_index isn't found when initializing the dictionary lookup AE.
>
> I also tried Pei's suggestion of cleaning and rebuilding. I tried both in eclipse (Project menu -> "clean...", then choose to clean all the project, and let eclipse automatically rebuild), and on the command-line ("mvn clean compile" from the root project).
>
> I'll comment on my attempt from the command-line here...
>
> I can see that it's trying to extract the dependency for "ctakes-resources-umls2011ab-3.1.0.jar". This jar file does have the rxnorm_index in the appropriate location, but the ctakes-dictionary-lookup/target/classes directory does not have any rxnorm_index directory. Again, this is true from a clean-then-build either from eclipse or the command-line.
>
> Here's a fragment from the maven output (note the line that starts with "Unpacking...").
>
> Here's the maven output:
>
> [INFO]
> ----------------------------------------------------------------------
> -- [INFO] Building Apache cTAKES dictionary lookup
> 3.1.0-incubating-SNAPSHOT [INFO]
> ----------------------------------------------------------------------
> --
> [INFO]
> [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @
> ctakes-dictionary-lookup --- [INFO] Deleting
> /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
> [INFO]
> [INFO] --- maven-remote-resources-plugin:1.3:process (default) @
> ctakes-dictionary-lookup --- [INFO] [INFO] ---
> maven-resources-plugin:2.5:resources (default-resources) @
> ctakes-dictionary-lookup --- [debug] execute contextualize [INFO]
> Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 80 resources
> [INFO] Copying 3 resources
> [INFO]
> [INFO] --- maven-dependency-plugin:2.6:unpack-dependencies
> (unpack-dependencies) @ ctakes-dictionary-lookup --- [INFO] Unpacking /Users/mcoarr/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes with includes "" and excludes ""
> [INFO]
> [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @
> ctakes-dictionary-lookup --- [INFO] Compiling 58 source files to
> /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
> /classes
>
> Thanks!
> Matt
>
> From: Tim Miller
> <timothy.miller@childrens.harvard.edu<mailto:timothy.miller@childrens.
> harvard.edu>>
> Reply-To:
> "ctakes-dev@incubator.apache.org<mailto:ctakes-dev@incubator.apache.or
> g>"
> <ctakes-dev@incubator.apache.org<mailto:ctakes-dev@incubator.apache.or
> g>>
> Date: Thursday, January 10, 2013 17:42
> To:
> "ctakes-dev@incubator.apache.org<mailto:ctakes-dev@incubator.apache.or
> g>"
> <ctakes-dev@incubator.apache.org<mailto:ctakes-dev@incubator.apache.or
> g>>
> Subject: Re: Failure on unpack-dependencies?
>
> I'm having some trouble with this issue on trunk using eclipse. When I
> try to run the default pipeline in the cvd it can't find the rxnorm_index:
Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup
problem with rxnorm_index]
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
I wonder if its worth it to update the instructions to just unzip it manually. Probably more complicated to try to do it automatically do it with the plugins...
Or remove the requirement to unpack jars (I think it was a Lucene limitation not be able to read from a jar file)
Sent from my iPhone
On Jan 18, 2013, at 1:32 PM, "Coarr, Matt" <mc...@mitre.org> wrote:
> Tim, did you ever manage to get this working? Does anyone else have any ideas on this problem?
>
> I'm trying to run the full pipeline on the ctakes trunk and I'm running into the same issue — rxnorm_index isn't found when initializing the dictionary lookup AE.
>
> I also tried Pei's suggestion of cleaning and rebuilding. I tried both in eclipse (Project menu -> "clean…", then choose to clean all the project, and let eclipse automatically rebuild), and on the command-line ("mvn clean compile" from the root project).
>
> I'll comment on my attempt from the command-line here…
>
> I can see that it's trying to extract the dependency for "ctakes-resources-umls2011ab-3.1.0.jar". This jar file does have the rxnorm_index in the appropriate location, but the ctakes-dictionary-lookup/target/classes directory does not have any rxnorm_index directory. Again, this is true from a clean-then-build either from eclipse or the command-line.
>
> Here's a fragment from the maven output (note the line that starts with "Unpacking…").
>
> Here's the maven output:
>
> [INFO] ------------------------------------------------------------------------
> [INFO] Building Apache cTAKES dictionary lookup 3.1.0-incubating-SNAPSHOT
> [INFO] ------------------------------------------------------------------------
> [INFO]
> [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-dictionary-lookup ---
> [INFO] Deleting /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
> [INFO]
> [INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-dictionary-lookup ---
> [INFO]
> [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-dictionary-lookup ---
> [debug] execute contextualize
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 80 resources
> [INFO] Copying 3 resources
> [INFO]
> [INFO] --- maven-dependency-plugin:2.6:unpack-dependencies (unpack-dependencies) @ ctakes-dictionary-lookup ---
> [INFO] Unpacking /Users/mcoarr/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes with includes "" and excludes ""
> [INFO]
> [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-dictionary-lookup ---
> [INFO] Compiling 58 source files to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes
>
> Thanks!
> Matt
>
> From: Tim Miller <ti...@childrens.harvard.edu>>
> Reply-To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
> Date: Thursday, January 10, 2013 17:42
> To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
> Subject: Re: Failure on unpack-dependencies?
>
> I'm having some trouble with this issue on trunk using eclipse. When I
> try to run the default pipeline in the cvd it can't find the rxnorm_index:
Re: Failure on unpack-dependencies?
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
For the command line, do a clean before compile
I.e $ mvn clean compile
Sent from my iPhone
On Jan 10, 2013, at 5:42 PM, "Tim Miller" <ti...@childrens.harvard.edu> wrote:
> I'm having some trouble with this issue on trunk using eclipse. When I try to run the default pipeline in the cvd it can't find the rxnorm_index:
>
> Caused by: java.io.FileNotFoundException:
> org/apache/ctakes/dictionary/lookup/rxnorm_index
> at
> org.apache.ctakes.core.resource.FileLocator.locateExplicitly(FileLocator.java:69)
> at
> org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:44)
> at
> org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:58)
> ... 59 more
>
> When I try to compile from the command line it says:
>
> [INFO]
> ------------------------------------------------------------------------
> [INFO] Building Apache cTAKES dictionary lookup
> 3.1.0-incubating-SNAPSHOT
> [INFO]
> ------------------------------------------------------------------------
> [INFO]
> [INFO] --- maven-remote-resources-plugin:1.3:process (default) @
> ctakes-dictionary-lookup ---
> [INFO]
> [INFO] --- maven-resources-plugin:2.5:resources (default-resources)
> @ ctakes-dictionary-lookup ---
> [debug] execute contextualize
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 54 resources
> [INFO] Copying 3 resources
> [INFO]
> [INFO] --- maven-dependency-plugin:2.6:unpack-dependencies
> (unpack-dependencies) @ ctakes-dictionary-lookup ---
> [INFO] ctakes-resources-umls2011ab-3.1.0.jar already exists in
> destination.
> [INFO]
> [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @
> ctakes-dictionary-lookup ---
> [INFO] Nothing to compile - all classes are up to date
> [INFO]
>
>
> -- so it says the resources are there, and I can see the downloaded jar in my .m2 directory, but they're not being unpacked for some reason (they are not in target/classes/.../ of dictionary-lookup as I think they are supposed to be). Anyone else with this problem? Any idea what's going on?
> Tim
>
>
> On 01/09/2013 05:20 PM, Karthik Sarma wrote:
>> I was able to check out the 3.0.0 branch and build + run it without
>> trouble. Will give the trunk another try
>>
>>
>>
>>
>>
>> --
>> Karthik Sarma
>> UCLA Medical Scientist Training Program Class of 20??
>> Member, UCLA Medical Imaging & Informatics Lab
>> Member, CA Delegation to the House of Delegates of the American Medical
>> Association
>> ksarma@ksarma.com
>> gchat: ksarma@gmail.com
>> linkedin: www.linkedin.com/in/ksarma
>>
>>
>> On Wed, Jan 9, 2013 at 1:46 PM, Masanz, James J. <Ma...@mayo.edu>wrote:
>>
>>> I did not get this error when I used eclipse's miport feature with maven
>>> from SCM.
>>> Everything built fine (The second time I tried a build)
>>> Note, I did a Maven->Update project... from within eclipse between the two
>>> builds.
>>>
>>> -- James
>>>
>>>
>>>> -----Original Message-----
>>>> From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of Karthik
>>>> Sarma
>>>> Sent: Tuesday, January 08, 2013 6:30 PM
>>>> To: cTAKES Developer List
>>>> Subject: Failure on unpack-dependencies?
>>>>
>>>> Hi folks,
>>>>
>>>> I was trying to get the trunk up and running on a new windows 8 machine
>>>> (completely clean). Installed jdk, eclipse (classic/juno), m2e, and
>>>> subversive. I used eclipse's import feature with maven from SCM. Checkout
>>>> was fine, but ctakes-dictionary-lookup was not able to build (as far as I
>>>> could tell, everything else built just fine. Here is the error:
>>>>
>>>> Execution unpack-dependencies of goal
>>>> org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-dependencies
>>>> failed: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.6 or
>>> one
>>>> of its dependencies could not be resolved: Failed to collect dependencies
>>>> for org.apache.maven.plugins:maven-dependency-plugin:jar:2.6 ()
>>>> (org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-
>>>> dependencies:unpack-dependencies:process-resources)
>>>> pom.xml /ctakes-dictionary-lookup line 82
>>>>
>>>> I did a few checks to try to diagnose the issue -- the pom seems to be
>>>> correct, and the m2e fix for unpack also seems to be correct. The plugin
>>>> itself (for umls) exists in my local repository, as does
>>> maven-dependency-
>>>> plugin 2.6. There aren't any spaces or other oddities in any of the
>>> paths.
>>>> I tried cleaning, re-acquiring the source, and even deleting eclipse and
>>>> starting from scratch, but alas, no dice.
>>>>
>>>> Is anyone else having a similar issue? Jenkins says everything should be
>>>> working fine. I should probably just try building without involving
>>>> eclipse at all, which I will do next.
>>>>
>>>>
>>>> Karthik
>>>>
>>>>
>>>> --
>>>> Karthik Sarma
>>>> UCLA Medical Scientist Training Program Class of 20??
>>>> Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to
>>>> the House of Delegates of the American Medical Association
>>>> ksarma@ksarma.com
>>>> gchat: ksarma@gmail.com
>>>> linkedin: www.linkedin.com/in/ksarma
>
Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup
problem with rxnorm_index]
Posted by "Coarr, Matt" <mc...@mitre.org>.
Thanks Tim, Sean, and Pei!
After a few full builds of ctakes from the command-line, it actually did the extraction.
If it happens again, I'll just manually extract it until the issue is resolved.
Thanks for the quick help!!
Matt
From: Tim Miller <ti...@childrens.harvard.edu>>
Reply-To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
Date: Friday, January 18, 2013 13:55
To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
Subject: Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup problem with rxnorm_index]
I can get it working with Pei's suggestion of doing mvn clean compile
from the command line. It is usually ok then even as I make other
changes to other projects, and then eventually at some point blows it
away (maybe when I do a project-wide maven update?).
Tim
Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup problem
with rxnorm_index]
Posted by Tim Miller <ti...@childrens.harvard.edu>.
I can get it working with Pei's suggestion of doing mvn clean compile
from the command line. It is usually ok then even as I make other
changes to other projects, and then eventually at some point blows it
away (maybe when I do a project-wide maven update?).
Tim
On 01/18/2013 01:32 PM, Coarr, Matt wrote:
> Tim, did you ever manage to get this working? Does anyone else have any ideas on this problem?
>
> I'm trying to run the full pipeline on the ctakes trunk and I'm running into the same issue — rxnorm_index isn't found when initializing the dictionary lookup AE.
>
> I also tried Pei's suggestion of cleaning and rebuilding. I tried both in eclipse (Project menu -> "clean…", then choose to clean all the project, and let eclipse automatically rebuild), and on the command-line ("mvn clean compile" from the root project).
>
> I'll comment on my attempt from the command-line here…
>
> I can see that it's trying to extract the dependency for "ctakes-resources-umls2011ab-3.1.0.jar". This jar file does have the rxnorm_index in the appropriate location, but the ctakes-dictionary-lookup/target/classes directory does not have any rxnorm_index directory. Again, this is true from a clean-then-build either from eclipse or the command-line.
>
> Here's a fragment from the maven output (note the line that starts with "Unpacking…").
>
> Here's the maven output:
>
> [INFO] ------------------------------------------------------------------------
> [INFO] Building Apache cTAKES dictionary lookup 3.1.0-incubating-SNAPSHOT
> [INFO] ------------------------------------------------------------------------
> [INFO]
> [INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-dictionary-lookup ---
> [INFO] Deleting /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
> [INFO]
> [INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-dictionary-lookup ---
> [INFO]
> [INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-dictionary-lookup ---
> [debug] execute contextualize
> [INFO] Using 'UTF-8' encoding to copy filtered resources.
> [INFO] Copying 80 resources
> [INFO] Copying 3 resources
> [INFO]
> [INFO] --- maven-dependency-plugin:2.6:unpack-dependencies (unpack-dependencies) @ ctakes-dictionary-lookup ---
> [INFO] Unpacking /Users/mcoarr/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes with includes "" and excludes ""
> [INFO]
> [INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-dictionary-lookup ---
> [INFO] Compiling 58 source files to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes
>
> Thanks!
> Matt
>
> From: Tim Miller <ti...@childrens.harvard.edu>>
> Reply-To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
> Date: Thursday, January 10, 2013 17:42
> To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
> Subject: Re: Failure on unpack-dependencies?
>
> I'm having some trouble with this issue on trunk using eclipse. When I
> try to run the default pipeline in the cvd it can't find the rxnorm_index:
Re: Failure on unpack-dependencies? [ctakes-dictionary-lookup
problem with rxnorm_index]
Posted by "Coarr, Matt" <mc...@mitre.org>.
Tim, did you ever manage to get this working? Does anyone else have any ideas on this problem?
I'm trying to run the full pipeline on the ctakes trunk and I'm running into the same issue — rxnorm_index isn't found when initializing the dictionary lookup AE.
I also tried Pei's suggestion of cleaning and rebuilding. I tried both in eclipse (Project menu -> "clean…", then choose to clean all the project, and let eclipse automatically rebuild), and on the command-line ("mvn clean compile" from the root project).
I'll comment on my attempt from the command-line here…
I can see that it's trying to extract the dependency for "ctakes-resources-umls2011ab-3.1.0.jar". This jar file does have the rxnorm_index in the appropriate location, but the ctakes-dictionary-lookup/target/classes directory does not have any rxnorm_index directory. Again, this is true from a clean-then-build either from eclipse or the command-line.
Here's a fragment from the maven output (note the line that starts with "Unpacking…").
Here's the maven output:
[INFO] ------------------------------------------------------------------------
[INFO] Building Apache cTAKES dictionary lookup 3.1.0-incubating-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] --- maven-clean-plugin:2.4.1:clean (default-clean) @ ctakes-dictionary-lookup ---
[INFO] Deleting /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target
[INFO]
[INFO] --- maven-remote-resources-plugin:1.3:process (default) @ ctakes-dictionary-lookup ---
[INFO]
[INFO] --- maven-resources-plugin:2.5:resources (default-resources) @ ctakes-dictionary-lookup ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 80 resources
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-dependency-plugin:2.6:unpack-dependencies (unpack-dependencies) @ ctakes-dictionary-lookup ---
[INFO] Unpacking /Users/mcoarr/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-umls2011ab/3.1.0/ctakes-resources-umls2011ab-3.1.0.jar to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes with includes "" and excludes ""
[INFO]
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @ ctakes-dictionary-lookup ---
[INFO] Compiling 58 source files to /work/medfacts/apache/svn/apache_trunk/ctakes-dictionary-lookup/target/classes
Thanks!
Matt
From: Tim Miller <ti...@childrens.harvard.edu>>
Reply-To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
Date: Thursday, January 10, 2013 17:42
To: "ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>" <ct...@incubator.apache.org>>
Subject: Re: Failure on unpack-dependencies?
I'm having some trouble with this issue on trunk using eclipse. When I
try to run the default pipeline in the cvd it can't find the rxnorm_index:
Re: Failure on unpack-dependencies?
Posted by Tim Miller <ti...@childrens.harvard.edu>.
I'm having some trouble with this issue on trunk using eclipse. When I
try to run the default pipeline in the cvd it can't find the rxnorm_index:
Caused by: java.io.FileNotFoundException:
org/apache/ctakes/dictionary/lookup/rxnorm_index
at
org.apache.ctakes.core.resource.FileLocator.locateExplicitly(FileLocator.java:69)
at
org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:44)
at
org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:58)
... 59 more
When I try to compile from the command line it says:
[INFO]
------------------------------------------------------------------------
[INFO] Building Apache cTAKES dictionary lookup
3.1.0-incubating-SNAPSHOT
[INFO]
------------------------------------------------------------------------
[INFO]
[INFO] --- maven-remote-resources-plugin:1.3:process (default) @
ctakes-dictionary-lookup ---
[INFO]
[INFO] --- maven-resources-plugin:2.5:resources (default-resources)
@ ctakes-dictionary-lookup ---
[debug] execute contextualize
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 54 resources
[INFO] Copying 3 resources
[INFO]
[INFO] --- maven-dependency-plugin:2.6:unpack-dependencies
(unpack-dependencies) @ ctakes-dictionary-lookup ---
[INFO] ctakes-resources-umls2011ab-3.1.0.jar already exists in
destination.
[INFO]
[INFO] --- maven-compiler-plugin:2.4:compile (default-compile) @
ctakes-dictionary-lookup ---
[INFO] Nothing to compile - all classes are up to date
[INFO]
-- so it says the resources are there, and I can see the downloaded jar
in my .m2 directory, but they're not being unpacked for some reason
(they are not in target/classes/.../ of dictionary-lookup as I think
they are supposed to be). Anyone else with this problem? Any idea
what's going on?
Tim
On 01/09/2013 05:20 PM, Karthik Sarma wrote:
> I was able to check out the 3.0.0 branch and build + run it without
> trouble. Will give the trunk another try
>
>
>
>
>
> --
> Karthik Sarma
> UCLA Medical Scientist Training Program Class of 20??
> Member, UCLA Medical Imaging & Informatics Lab
> Member, CA Delegation to the House of Delegates of the American Medical
> Association
> ksarma@ksarma.com
> gchat: ksarma@gmail.com
> linkedin: www.linkedin.com/in/ksarma
>
>
> On Wed, Jan 9, 2013 at 1:46 PM, Masanz, James J. <Ma...@mayo.edu>wrote:
>
>> I did not get this error when I used eclipse's miport feature with maven
>> from SCM.
>> Everything built fine (The second time I tried a build)
>> Note, I did a Maven->Update project... from within eclipse between the two
>> builds.
>>
>> -- James
>>
>>
>>> -----Original Message-----
>>> From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of Karthik
>>> Sarma
>>> Sent: Tuesday, January 08, 2013 6:30 PM
>>> To: cTAKES Developer List
>>> Subject: Failure on unpack-dependencies?
>>>
>>> Hi folks,
>>>
>>> I was trying to get the trunk up and running on a new windows 8 machine
>>> (completely clean). Installed jdk, eclipse (classic/juno), m2e, and
>>> subversive. I used eclipse's import feature with maven from SCM. Checkout
>>> was fine, but ctakes-dictionary-lookup was not able to build (as far as I
>>> could tell, everything else built just fine. Here is the error:
>>>
>>> Execution unpack-dependencies of goal
>>> org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-dependencies
>>> failed: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.6 or
>> one
>>> of its dependencies could not be resolved: Failed to collect dependencies
>>> for org.apache.maven.plugins:maven-dependency-plugin:jar:2.6 ()
>>> (org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-
>>> dependencies:unpack-dependencies:process-resources)
>>> pom.xml /ctakes-dictionary-lookup line 82
>>>
>>> I did a few checks to try to diagnose the issue -- the pom seems to be
>>> correct, and the m2e fix for unpack also seems to be correct. The plugin
>>> itself (for umls) exists in my local repository, as does
>> maven-dependency-
>>> plugin 2.6. There aren't any spaces or other oddities in any of the
>> paths.
>>> I tried cleaning, re-acquiring the source, and even deleting eclipse and
>>> starting from scratch, but alas, no dice.
>>>
>>> Is anyone else having a similar issue? Jenkins says everything should be
>>> working fine. I should probably just try building without involving
>>> eclipse at all, which I will do next.
>>>
>>>
>>> Karthik
>>>
>>>
>>> --
>>> Karthik Sarma
>>> UCLA Medical Scientist Training Program Class of 20??
>>> Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to
>>> the House of Delegates of the American Medical Association
>>> ksarma@ksarma.com
>>> gchat: ksarma@gmail.com
>>> linkedin: www.linkedin.com/in/ksarma
Re: Failure on unpack-dependencies?
Posted by Karthik Sarma <ks...@ksarma.com>.
I was able to check out the 3.0.0 branch and build + run it without
trouble. Will give the trunk another try
--
Karthik Sarma
UCLA Medical Scientist Training Program Class of 20??
Member, UCLA Medical Imaging & Informatics Lab
Member, CA Delegation to the House of Delegates of the American Medical
Association
ksarma@ksarma.com
gchat: ksarma@gmail.com
linkedin: www.linkedin.com/in/ksarma
On Wed, Jan 9, 2013 at 1:46 PM, Masanz, James J. <Ma...@mayo.edu>wrote:
> I did not get this error when I used eclipse's miport feature with maven
> from SCM.
> Everything built fine (The second time I tried a build)
> Note, I did a Maven->Update project... from within eclipse between the two
> builds.
>
> -- James
>
>
> > -----Original Message-----
> > From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of Karthik
> > Sarma
> > Sent: Tuesday, January 08, 2013 6:30 PM
> > To: cTAKES Developer List
> > Subject: Failure on unpack-dependencies?
> >
> > Hi folks,
> >
> > I was trying to get the trunk up and running on a new windows 8 machine
> > (completely clean). Installed jdk, eclipse (classic/juno), m2e, and
> > subversive. I used eclipse's import feature with maven from SCM. Checkout
> > was fine, but ctakes-dictionary-lookup was not able to build (as far as I
> > could tell, everything else built just fine. Here is the error:
> >
> > Execution unpack-dependencies of goal
> > org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-dependencies
> > failed: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.6 or
> one
> > of its dependencies could not be resolved: Failed to collect dependencies
> > for org.apache.maven.plugins:maven-dependency-plugin:jar:2.6 ()
> > (org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-
> > dependencies:unpack-dependencies:process-resources)
> > pom.xml /ctakes-dictionary-lookup line 82
> >
> > I did a few checks to try to diagnose the issue -- the pom seems to be
> > correct, and the m2e fix for unpack also seems to be correct. The plugin
> > itself (for umls) exists in my local repository, as does
> maven-dependency-
> > plugin 2.6. There aren't any spaces or other oddities in any of the
> paths.
> > I tried cleaning, re-acquiring the source, and even deleting eclipse and
> > starting from scratch, but alas, no dice.
> >
> > Is anyone else having a similar issue? Jenkins says everything should be
> > working fine. I should probably just try building without involving
> > eclipse at all, which I will do next.
> >
> >
> > Karthik
> >
> >
> > --
> > Karthik Sarma
> > UCLA Medical Scientist Training Program Class of 20??
> > Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to
> > the House of Delegates of the American Medical Association
> > ksarma@ksarma.com
> > gchat: ksarma@gmail.com
> > linkedin: www.linkedin.com/in/ksarma
>
RE: Failure on unpack-dependencies?
Posted by "Masanz, James J." <Ma...@mayo.edu>.
I did not get this error when I used eclipse's miport feature with maven from SCM.
Everything built fine (The second time I tried a build)
Note, I did a Maven->Update project... from within eclipse between the two builds.
-- James
> -----Original Message-----
> From: ksarma@gmail.com [mailto:ksarma@gmail.com] On Behalf Of Karthik
> Sarma
> Sent: Tuesday, January 08, 2013 6:30 PM
> To: cTAKES Developer List
> Subject: Failure on unpack-dependencies?
>
> Hi folks,
>
> I was trying to get the trunk up and running on a new windows 8 machine
> (completely clean). Installed jdk, eclipse (classic/juno), m2e, and
> subversive. I used eclipse's import feature with maven from SCM. Checkout
> was fine, but ctakes-dictionary-lookup was not able to build (as far as I
> could tell, everything else built just fine. Here is the error:
>
> Execution unpack-dependencies of goal
> org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-dependencies
> failed: Plugin org.apache.maven.plugins:maven-dependency-plugin:2.6 or one
> of its dependencies could not be resolved: Failed to collect dependencies
> for org.apache.maven.plugins:maven-dependency-plugin:jar:2.6 ()
> (org.apache.maven.plugins:maven-dependency-plugin:2.6:unpack-
> dependencies:unpack-dependencies:process-resources)
> pom.xml /ctakes-dictionary-lookup line 82
>
> I did a few checks to try to diagnose the issue -- the pom seems to be
> correct, and the m2e fix for unpack also seems to be correct. The plugin
> itself (for umls) exists in my local repository, as does maven-dependency-
> plugin 2.6. There aren't any spaces or other oddities in any of the paths.
> I tried cleaning, re-acquiring the source, and even deleting eclipse and
> starting from scratch, but alas, no dice.
>
> Is anyone else having a similar issue? Jenkins says everything should be
> working fine. I should probably just try building without involving
> eclipse at all, which I will do next.
>
>
> Karthik
>
>
> --
> Karthik Sarma
> UCLA Medical Scientist Training Program Class of 20??
> Member, UCLA Medical Imaging & Informatics Lab Member, CA Delegation to
> the House of Delegates of the American Medical Association
> ksarma@ksarma.com
> gchat: ksarma@gmail.com
> linkedin: www.linkedin.com/in/ksarma