R backend OSX Mavericks

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R backend OSX Mavericks

sammeek
Hi Board,

I am attempting to run the R backend on OSX using the provided demo org.n52.wps.server.r.intersection.

The process appears to work and produces the correct result, but will not return it to the Java client. The server side error is as follows:

2014-08-12 14:20:11,912 [pool-5-thread-10] INFO  org.n52.wps.io.data.GenericFileData: Writing temp data to: /usr/local/apache-tomcat-7.0.54/temp/tmp6cb7fcf7-f098-4d54-99e5-8926c9aed369
2014-08-12 14:20:12,195 [pool-5-thread-10] ERROR org.n52.wps.io.data.GenericFileData: Could not unzip the archive to /usr/local/apache-tomcat-7.0.54/temp/tmp6cb7fcf7-f098-4d54-99e5-8926c9aed369
java.io.EOFException: Unexpected end of ZLIB input stream
        at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
        at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
        at java.util.zip.ZipInputStream.read(ZipInputStream.java:194)
        at java.util.zip.ZipInputStream.closeEntry(ZipInputStream.java:140)
        at java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:118)
        at org.n52.wps.io.data.GenericFileData.unzipData(GenericFileData.java:346)
        at org.n52.wps.io.data.GenericFileData.writeData(GenericFileData.java:319)
        at org.n52.wps.io.data.GenericFileData.getAsGTVectorDataBinding(GenericFileData.java:412)
        at org.n52.wps.server.r.GenericRProcess.parseOutput(GenericRProcess.java:945)
        at org.n52.wps.server.r.GenericRProcess.run(GenericRProcess.java:387)
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:637)
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:91)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
2014-08-12 14:20:12,196 [pool-5-thread-10] INFO  org.n52.wps.io.data.GenericFileData: Temp file is: null
2014-08-12 14:20:12,196 [pool-5-thread-10] ERROR org.n52.wps.server.request.ExecuteRequest: Exception/Error while executing ExecuteRequest for org.n52.wps.server.r.intersection: java.lang.NullPointerException
2014-08-12 14:20:12,196 [pool-5-thread-10] INFO  org.n52.wps.commons.context.ExecutionContextFactory: Context unregistered
2014-08-12 14:20:12,196 [http-bio-8080-exec-7] WARN  org.n52.wps.server.handler.RequestHandler: exception while handling ExecuteRequest.
2014-08-12 14:20:12,198 [http-bio-8080-exec-7] ERROR org.n52.wps.server.handler.RequestHandler: exception handling ExecuteRequest.
org.n52.wps.server.ExceptionReport: Error while executing the embedded process for: org.n52.wps.server.r.intersection
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:668) ~[52n-wps-server-3.2.0.jar:na]
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:91) ~[52n-wps-server-3.2.0.jar:na]
        at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_11]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[na:1.8.0_11]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_11]
        at java.lang.Thread.run(Thread.java:745) [na:1.8.0_11]
Caused by: java.lang.NullPointerException: null
        at java.io.File.<init>(File.java:277) ~[na:1.8.0_11]
        at org.n52.wps.io.data.GenericFileData.getAsGTVectorDataBinding(GenericFileData.java:414) ~[52n-wps-io-impl-3.2.0.jar:na]
        at org.n52.wps.server.r.GenericRProcess.parseOutput(GenericRProcess.java:945) ~[52n-wps-r-3.2.0.jar:na]
        at org.n52.wps.server.r.GenericRProcess.run(GenericRProcess.java:387) ~[52n-wps-r-3.2.0.jar:na]
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:637) ~[52n-wps-server-3.2.0.jar:na]
        ... 5 common frames omitted
2014-08-12 14:20:12,198 [http-bio-8080-exec-7] DEBUG org.n52.wps.server.WebProcessingService: org.n52.wps.server.ExceptionReport: Error while executing the embedded process for: org.n52.wps.server.r.intersection
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Re: R backend OSX Mavericks

Daniel
Hi Sam!

Am 12.08.2014 um 15:21 schrieb sammeek:
> I am attempting to run the R backend on OSX using the provided demo
> org.n52.wps.server.r.intersection.

Thanks for you interest in WPS4R!

> The process appears to work and produces the correct result,

How do you know that?

Also, which version of WPS are you using? What is your configuration of
the LocalRAlgorithmRepository?

 > but will not
> return it to the Java client. The server side error is as follows:
>
> 2014-08-12 14:20:11,912 [pool-5-thread-10] INFO
> org.n52.wps.io.data.GenericFileData: Writing temp data to:
> /usr/local/apache-tomcat-7.0.54/temp/tmp6cb7fcf7-f098-4d54-99e5-8926c9aed369

Can you go into this directory and see if the file is actually created?

> 2014-08-12 14:20:12,195 [pool-5-thread-10] ERROR
> org.n52.wps.io.data.GenericFileData: Could not unzip the archive to
> /usr/local/apache-tomcat-7.0.54/temp/tmp6cb7fcf7-f098-4d54-99e5-8926c9aed369

What are the read/write permissions on that directory?

If the file is created correctly then we at least know there is no
rights issue.

/Daniel

> java.io.EOFException: Unexpected end of ZLIB input stream
> at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
> at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
> at java.util.zip.ZipInputStream.read(ZipInputStream.java:194)
> at java.util.zip.ZipInputStream.closeEntry(ZipInputStream.java:140)
> at java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:118)
> at org.n52.wps.io.data.GenericFileData.unzipData(GenericFileData.java:346)
> at org.n52.wps.io.data.GenericFileData.writeData(GenericFileData.java:319)
> at
> org.n52.wps.io.data.GenericFileData.getAsGTVectorDataBinding(GenericFileData.java:412)
> at
> org.n52.wps.server.r.GenericRProcess.parseOutput(GenericRProcess.java:945)
> at org.n52.wps.server.r.GenericRProcess.run(GenericRProcess.java:387)
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:637)
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:91)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> 2014-08-12 14:20:12,196 [pool-5-thread-10] INFO
> org.n52.wps.io.data.GenericFileData: Temp file is: null
> 2014-08-12 14:20:12,196 [pool-5-thread-10] ERROR
> org.n52.wps.server.request.ExecuteRequest: Exception/Error while executing
> ExecuteRequest for org.n52.wps.server.r.intersection:
> java.lang.NullPointerException
> 2014-08-12 14:20:12,196 [pool-5-thread-10] INFO
> org.n52.wps.commons.context.ExecutionContextFactory: Context unregistered
> 2014-08-12 14:20:12,196 [http-bio-8080-exec-7] WARN
> org.n52.wps.server.handler.RequestHandler: exception while handling
> ExecuteRequest.
> 2014-08-12 14:20:12,198 [http-bio-8080-exec-7] ERROR
> org.n52.wps.server.handler.RequestHandler: exception handling
> ExecuteRequest.
> org.n52.wps.server.ExceptionReport: Error while executing the embedded
> process for: org.n52.wps.server.r.intersection
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:668)
> ~[52n-wps-server-3.2.0.jar:na]
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:91)
> ~[52n-wps-server-3.2.0.jar:na]
> at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_11]
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> ~[na:1.8.0_11]
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> ~[na:1.8.0_11]
> at java.lang.Thread.run(Thread.java:745) [na:1.8.0_11]
> Caused by: java.lang.NullPointerException: null
> at java.io.File.<init>(File.java:277) ~[na:1.8.0_11]
> at
> org.n52.wps.io.data.GenericFileData.getAsGTVectorDataBinding(GenericFileData.java:414)
> ~[52n-wps-io-impl-3.2.0.jar:na]
> at
> org.n52.wps.server.r.GenericRProcess.parseOutput(GenericRProcess.java:945)
> ~[52n-wps-r-3.2.0.jar:na]
> at org.n52.wps.server.r.GenericRProcess.run(GenericRProcess.java:387)
> ~[52n-wps-r-3.2.0.jar:na]
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:637)
> ~[52n-wps-server-3.2.0.jar:na]
> ... 5 common frames omitted
> 2014-08-12 14:20:12,198 [http-bio-8080-exec-7] DEBUG
> org.n52.wps.server.WebProcessingService: org.n52.wps.server.ExceptionReport:
> Error while executing the embedded process for:
> org.n52.wps.server.r.intersection
>
>
>
>
> --
> View this message in context: http://geoprocessing.forum.52north.org/R-backend-OSX-Mavericks-tp4025748.html
> Sent from the 52° North - Geoprocessing Community Forum mailing list archive at Nabble.com.
> _______________________________________________
> Geoprocessingservices mailing list
> [hidden email]
> http://list.52north.org/mailman/listinfo/geoprocessingservices
> http://geoprocessing.forum.52north.org
>


--
Daniel Nüst
52°North Initiative for Geospatial Open Source Software GmbH
Martin-Luther-King-Weg 24
48155 Münster, Germany
E-Mail: [hidden email]
Fon: +49-(0)-251–396371-36
Fax: +49-(0)-251–396371-11

http://52north.org/
Twitter: @FiveTwoN

General Managers: Dr. Albert Remke, Dr. Andreas Wytzisk
Local Court Muenster HRB 10849
_______________________________________________
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Re: R backend OSX Mavericks

sammeek
Hi Daniel,

I believe that I have found the problem, I just need the solution.

Basically, the WPS is looking in my normal temp file for the Zip that has been generated (/tomcat7/temp/), but the WPS is writing the Zip to another folder (/tomcat7/webapps/wps/R/working/). I have had a hunt around I can't find the setting to rectify this, ideally, I would like to use /tomcat7/temp/ as the working directory for everything. Any ideas?

Thanks

Sam
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Re: R backend OSX Mavericks

Daniel
Hi Sam!

Am 13.08.2014 um 17:33 schrieb sammeek:
> I believe that I have found the problem, I just need the solution.
>
> Basically, the WPS is looking in my normal temp file for the Zip that has
> been generated (/tomcat7/temp/), but the WPS is writing the Zip to another
> folder (/tomcat7/webapps/wps/R/working/). I have had a hunt around I can't
> find the setting to rectify this, ideally, I would like to use
> /tomcat7/temp/ as the working directory for everything. Any ideas?

Which version of the WPS are you using?


There are several options for working directory configuration, see the
parameter "R_wdStrategy" at
https://wiki.52north.org/bin/view/Geostatistics/WPS4RDocumentation#Configuration_parameters

What is it set to now?

Try manualbasedir.


Hope this helps,
Daniel

>
>
>
> --
> View this message in context: http://geoprocessing.forum.52north.org/R-backend-OSX-Mavericks-tp4025748p4025750.html
> Sent from the 52° North - Geoprocessing Community Forum mailing list archive at Nabble.com.
> _______________________________________________
> Geoprocessingservices mailing list
> [hidden email]
> http://list.52north.org/mailman/listinfo/geoprocessingservices
> http://geoprocessing.forum.52north.org
>


--
Daniel Nüst
52°North Initiative for Geospatial Open Source Software GmbH
Martin-Luther-King-Weg 24
48155 Münster, Germany
E-Mail: [hidden email]
Fon: +49-(0)-251–396371-36
Fax: +49-(0)-251–396371-11

http://52north.org/
Twitter: @FiveTwoN

General Managers: Dr. Albert Remke, Dr. Andreas Wytzisk
Local Court Muenster HRB 10849
_______________________________________________
Geoprocessingservices mailing list
[hidden email]
http://list.52north.org/mailman/listinfo/geoprocessingservices
http://geoprocessing.forum.52north.org
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Re: R backend OSX Mavericks

sammeek
Hi Daniel,

Thanks for the speedy reply. I am using version 3.2 of the software.

I have done as you suggest and it appears as though the result is being written to the correct directory, but I am still getting the following error:

2014-08-14 10:17:12,330 [pool-5-thread-1] INFO  org.n52.wps.io.data.GenericFileData: Not all files are available, but the available ones are zipped.
2014-08-14 10:17:12,336 [pool-5-thread-1] INFO  org.n52.wps.io.data.GenericFileData: Writing temp data to: /usr/local/apache-tomcat-7.0.54/temp/tmpeb7f19f4-d2f8-4756-be37-6791ccd0a205
2014-08-14 10:17:12,825 [pool-5-thread-1] ERROR org.n52.wps.io.data.GenericFileData: Could not unzip the archive to /usr/local/apache-tomcat-7.0.54/temp/tmpeb7f19f4-d2f8-4756-be37-6791ccd0a205
java.io.EOFException: Unexpected end of ZLIB input stream2014-08-14 10:17:12,826 [pool-5-thread-1] INFO  org.n52.wps.io.data.GenericFileData: Temp file is: null
2014-08-14 10:17:12,826 [pool-5-thread-1] ERROR org.n52.wps.server.request.ExecuteRequest: Exception/Error while executing ExecuteRequest for org.n52.wps.server.r.intersection: java.lang.NullPointerException

        at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
        at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
        at java.util.zip.ZipInputStream.read(ZipInputStream.java:194)
        at java.util.zip.ZipInputStream.closeEntry(ZipInputStream.java:140)
        at java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:118)
        at org.n52.wps.io.data.GenericFileData.unzipData(GenericFileData.java:346)
        at org.n52.wps.io.data.GenericFileData.writeData(GenericFileData.java:319)
        at org.n52.wps.io.data.GenericFileData.getAsGTVectorDataBinding(GenericFileData.java:412)
        at org.n52.wps.server.r.GenericRProcess.parseOutput(GenericRProcess.java:945)
        at org.n52.wps.server.r.GenericRProcess.run(GenericRProcess.java:387)
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:637)
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:91)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
2014-08-14 10:17:12,834 [pool-5-thread-1] INFO  org.n52.wps.commons.context.ExecutionContextFactory: Context unregistered
2014-08-14 10:17:12,835 [http-bio-8080-exec-8] WARN  org.n52.wps.server.handler.RequestHandler: exception while handling ExecuteRequest.
2014-08-14 10:17:12,836 [http-bio-8080-exec-8] ERROR org.n52.wps.server.handler.RequestHandler: exception handling ExecuteRequest.
org.n52.wps.server.ExceptionReport: Error while executing the embedded process for: org.n52.wps.server.r.intersection
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:668) ~[52n-wps-server-3.2.0.jar:na]
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:91) ~[52n-wps-server-3.2.0.jar:na]
        at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_11]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[na:1.8.0_11]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_11]
        at java.lang.Thread.run(Thread.java:745) [na:1.8.0_11]
Caused by: java.lang.NullPointerException: null
        at java.io.File.<init>(File.java:277) ~[na:1.8.0_11]
        at org.n52.wps.io.data.GenericFileData.getAsGTVectorDataBinding(GenericFileData.java:414) ~[52n-wps-io-impl-3.2.0.jar:na]
        at org.n52.wps.server.r.GenericRProcess.parseOutput(GenericRProcess.java:945) ~[52n-wps-r-3.2.0.jar:na]
        at org.n52.wps.server.r.GenericRProcess.run(GenericRProcess.java:387) ~[52n-wps-r-3.2.0.jar:na]
        at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:637) ~[52n-wps-server-3.2.0.jar:na]
        ... 5 common frames omitted
2014-08-14 10:17:12,836 [http-bio-8080-exec-8] DEBUG org.n52.wps.server.WebProcessingService: org.n52.wps.server.ExceptionReport: Error while executing the embedded process for: org.n52.wps.server.r.intersection

The config is as follows:

R_Datatype_Config R/R_Datatype.conf
R_wdName /usr/local/apache-tomcat-7.0.54/temp
R_wdStrategy manualbasedir
Resource_Dir R/resources
Rserve_Host localhost
Rserve_Port 6311
Script_Dir R/scripts


Thanks

Sam
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Re: R backend OSX Mavericks

Daniel
Am 14.08.2014 um 11:21 schrieb sammeek:
> Thanks for the speedy reply. I am using version 3.2 of the software.

There was a new version released a few days back, 3.3.0 - I strongly
recommend updating to that version.

> I have done as you suggest and it appears as though the result is being
> written to the correct directory, but I am still getting the following
> error:
>
> 2014-08-14 10:17:12,330 [pool-5-thread-1] INFO
> org.n52.wps.io.data.GenericFileData: Not all files are available, but the
> available ones are zipped.
> 2014-08-14 10:17:12,336 [pool-5-thread-1] INFO
> org.n52.wps.io.data.GenericFileData: Writing temp data to:
> /usr/local/apache-tomcat-7.0.54/temp/tmpeb7f19f4-d2f8-4756-be37-6791ccd0a205
> 2014-08-14 10:17:12,825 [pool-5-thread-1] ERROR
> org.n52.wps.io.data.GenericFileData: Could not unzip the archive to
> /usr/local/apache-tomcat-7.0.54/temp/tmpeb7f19f4-d2f8-4756-be37-6791ccd0a205
> java.io.EOFException: Unexpected end of ZLIB input stream2014-08-14
> 10:17:12,826 [pool-5-thread-1] INFO  org.n52.wps.io.data.GenericFileData:
> Temp file is: null
> 2014-08-14 10:17:12,826 [pool-5-thread-1] ERROR
> org.n52.wps.server.request.ExecuteRequest: Exception/Error while executing
> ExecuteRequest for org.n52.wps.server.r.intersection:
> java.lang.NullPointerException
>
> at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:240)
> at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
> at java.util.zip.ZipInputStream.read(ZipInputStream.java:194)
> at java.util.zip.ZipInputStream.closeEntry(ZipInputStream.java:140)
> at java.util.zip.ZipInputStream.getNextEntry(ZipInputStream.java:118)
> at org.n52.wps.io.data.GenericFileData.unzipData(GenericFileData.java:346)
> at org.n52.wps.io.data.GenericFileData.writeData(GenericFileData.java:319)
> at
> org.n52.wps.io.data.GenericFileData.getAsGTVectorDataBinding(GenericFileData.java:412)
> at
> org.n52.wps.server.r.GenericRProcess.parseOutput(GenericRProcess.java:945)
> at org.n52.wps.server.r.GenericRProcess.run(GenericRProcess.java:387)
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:637)
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:91)
> at java.util.concurrent.FutureTask.run(FutureTask.java:266)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> 2014-08-14 10:17:12,834 [pool-5-thread-1] INFO
> org.n52.wps.commons.context.ExecutionContextFactory: Context unregistered
> 2014-08-14 10:17:12,835 [http-bio-8080-exec-8] WARN
> org.n52.wps.server.handler.RequestHandler: exception while handling
> ExecuteRequest.
> 2014-08-14 10:17:12,836 [http-bio-8080-exec-8] ERROR
> org.n52.wps.server.handler.RequestHandler: exception handling
> ExecuteRequest.
> org.n52.wps.server.ExceptionReport: Error while executing the embedded
> process for: org.n52.wps.server.r.intersection
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:668)
> ~[52n-wps-server-3.2.0.jar:na]
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:91)
> ~[52n-wps-server-3.2.0.jar:na]
> at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_11]
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> ~[na:1.8.0_11]
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> ~[na:1.8.0_11]
> at java.lang.Thread.run(Thread.java:745) [na:1.8.0_11]
> Caused by: java.lang.NullPointerException: null
> at java.io.File.<init>(File.java:277) ~[na:1.8.0_11]
> at
> org.n52.wps.io.data.GenericFileData.getAsGTVectorDataBinding(GenericFileData.java:414)
> ~[52n-wps-io-impl-3.2.0.jar:na]
> at
> org.n52.wps.server.r.GenericRProcess.parseOutput(GenericRProcess.java:945)
> ~[52n-wps-r-3.2.0.jar:na]
> at org.n52.wps.server.r.GenericRProcess.run(GenericRProcess.java:387)
> ~[52n-wps-r-3.2.0.jar:na]
> at org.n52.wps.server.request.ExecuteRequest.call(ExecuteRequest.java:637)
> ~[52n-wps-server-3.2.0.jar:na]
> ... 5 common frames omitted
> 2014-08-14 10:17:12,836 [http-bio-8080-exec-8] DEBUG
> org.n52.wps.server.WebProcessingService: org.n52.wps.server.ExceptionReport:
> Error while executing the embedded process for:
> org.n52.wps.server.r.intersection
>
> The config is as follows:
>
> R_Datatype_Config R/R_Datatype.conf
> R_wdName /usr/local/apache-tomcat-7.0.54/temp
> R_wdStrategy manualbasedir
> Resource_Dir R/resources
> Rserve_Host localhost
> Rserve_Port 6311
> Script_Dir R/scripts

Can you please try with the latest version? There were quite a few fixed
bugs, and you will not have to change your R scripts.

Also, can you post a minimal example R script [1] that replicates the
problem?

/Daniel

[1]
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

--
Daniel Nüst
52°North Initiative for Geospatial Open Source Software GmbH
Martin-Luther-King-Weg 24
48155 Münster, Germany
E-Mail: [hidden email]
Fon: +49-(0)-251–396371-36
Fax: +49-(0)-251–396371-11

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Twitter: @FiveTwoN

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Re: R backend OSX Mavericks

sammeek
Hi Daniel,

I have done as suggested and completed the upgrade to 3.3. It has solved the problem on the backend as the  server is now producing and unzipping data in the correct location. However, I am using the java client and getting issues with returning the data. I have attached the client code and have tried returning GTVectorDataBinding and ShapefileBinding and they both have issues, the posted client class produced the following error:

org.xml.sax.SAXParseException; Premature end of file.
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:195)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.determineFeatureTypeSchema(GML3BasicParser.java:283)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.parseFeatureCollection(GML3BasicParser.java:134)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.parseXML(GML3BasicParser.java:119)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.parse(GML3BasicParser.java:104)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.parse(GML3BasicParser.java:80)
        at org.n52.WPSExample.ExecuteResponseAnalyser.parseProcessOutput(ExecuteResponseAnalyser.java:240)
        at org.n52.WPSExample.ExecuteResponseAnalyser.getComplexData(ExecuteResponseAnalyser.java:89)
        at pillar.lbs.PositionQualityClient.executeProcess(PositionQualityClient.java:199)
        at pillar.lbs.PositionQualityClient.testExecute(PositionQualityClient.java:67)
        at pillar.lbs.PositionQualityClient.main(PositionQualityClient.java:213)
java.lang.IllegalArgumentException: org.xml.sax.SAXParseException; Premature end of file.
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.determineFeatureTypeSchema(GML3BasicParser.java:293)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.parseFeatureCollection(GML3BasicParser.java:134)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.parseXML(GML3BasicParser.java:119)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.parse(GML3BasicParser.java:104)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.parse(GML3BasicParser.java:80)
        at org.n52.WPSExample.ExecuteResponseAnalyser.parseProcessOutput(ExecuteResponseAnalyser.java:240)
        at org.n52.WPSExample.ExecuteResponseAnalyser.getComplexData(ExecuteResponseAnalyser.java:89)
        at pillar.lbs.PositionQualityClient.executeProcess(PositionQualityClient.java:199)
        at pillar.lbs.PositionQualityClient.testExecute(PositionQualityClient.java:67)
        at pillar.lbs.PositionQualityClient.main(PositionQualityClient.java:213)
Caused by: org.xml.sax.SAXParseException; Premature end of file.
        at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:392)
        at javax.xml.parsers.SAXParser.parse(SAXParser.java:195)
        at org.n52.wps.io.datahandler.parser.GML3BasicParser.determineFeatureTypeSchema(GML3BasicParser.java:283)
        ... 9 more

Any idea why?

SamPositionQualityClient.javageo_poly-intersection.R
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Re: R backend OSX Mavericks

BenjaminPross
Hi Sam,

There is another bug in the ExecuteResponseAnalyser. I see that the package name of the one you are using differs from the one shipped by us. Does that mean that you are using your own version of the class? I could then point you to the line that has to be modified.

Cheers,

Benjamin
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Re: R backend OSX Mavericks

sammeek
Hi Benjamin,

I have my own version of the class from a previous bug fix. Could you please tell me the line that needs to be modified?

Thanks

Sam
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Re: R backend OSX Mavericks

BenjaminPross
Ok, in the method parseProcessOutput you will have to change

complexDataContent = XMLUtil.nodeToString(processOutput.getData().getComplexData().getDomNode().getFirstChild());

to

complexDataContent = XMLUtil.nodeToString(processOutput.getData().getComplexData().getDomNode().getChildNodes().item(1));

Cheers,

Benjamin
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Re: R backend OSX Mavericks

sammeek
All working perfectly, thanks for the assist.

Sam