[BioC] Issues with RWebServices on MacOSX, ant rservices-test fails (1)

[Martin Morgan]

On 02/23/2010 05:04 AM, Michael Dondrup wrote:
> Hi,
> 

> after I installed SJava on MacOS with lots of help from this list, I
am trying to approach my original aim of
> getting RWebServices to run on the mac. I have run into some
> problems
again, maybe because this platform
> might not really be supported yet, or maybe I forgot to set one
environment variable.
> 
> I was able to resolve the first issue, but the second issue seems to
be more difficult:

Hi Michael --

Yes, I made a fix to the development version of RWebServices and will
port it to the release version when I have a chance to test on a mac. A
quick fix more approximating the change I made, rather than editing the
file, is along the lines of

LD_LIBRARY_PATH=/Library/Frameworks/R.framework/Resources/library/SJava/libs/x86_64:$LD_LIBRARY_PATH
ant rservices-test

What about the second problem?

Martin

> 
> Issue 1:
> 
> According to the manual (Installing and testing RWebServices) I installed the required software:
> I followed the manual to section 2, point 3. (ant basic-prop -- success).
> In the console I type:   
> Seneca:tmp mdondrup$  ant rservices-test
> Buildfile: build.xml
>      [echo]  RWebservicesHome : /Users/mdondrup/Library/R/2.10/library/RWebServices 
> 
> -check-for-RJava.jar:
> 
> -build-RJava.jar:
> 
> rservices-clean:
> 
> rservices-compile:
>     [javac] Compiling 12 source files to /Users/mdondrup/tmp/test/bin
> 
> rservices-test:
>     [junit] Test org.bioconductor.packages.rservices.CLevelConverterTest FAILED
>     [junit] Test org.bioconductor.packages.rservices.RClassTest FAILED
>     [junit] Test org.bioconductor.packages.rservices.RFileReferencesTest FAILED
>     [junit] Test org.bioconductor.packages.rservices.RJFileReferencesTest FAILED
>     [junit] Test org.bioconductor.packages.rservices.RJTypeTest FAILED
>     [junit] Test org.bioconductor.packages.rservices.RObjectsTest FAILED
>     [junit] Test org.bioconductor.packages.rservices.SJavaTypeTest FAILED
>      [echo] ===== See the directory '/Users/mdondrup/tmp/test/output' for more information ====
> 
> BUILD SUCCESSFUL
> Total time: 6 seconds
> 
> The test output contains the following:
> Testcase: org.bioconductor.packages.rservices.RClassTest took 0 sec
>         Caused an ERROR
> no RInterpreter in java.library.path
> java.lang.UnsatisfiedLinkError: no RInterpreter in java.library.path
>         at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1792)
>         at java.lang.Runtime.loadLibrary0(Runtime.java:823)
>         at java.lang.System.loadLibrary(System.java:1045)
>         at org.omegahat.R.Java.ROmegahatInterpreter.<clinit>(Unknown Source)
>         at org.bioconductor.packages.rservices.TypeTestUtil.setupR(Unknown Source)
> 
> partial solution:
> 
> The libRInterpreter.dylib library is not found, so edit:
>  ./Library/R/2.10/library/RWebServices/unitTests/build.xml 
> this is the ant script that runs the tests
> after line 17, add the location where the dynamic libraries are:
> 
>  <junit fork="yes" haltonfailure="no" dir="${test.dir}/output">
> +    <jvmarg value="-Djava.library.path=/Library/Frameworks/R.framework/Resources/library/SJava/libs/x86_64/"/>
>         <batchtest todir="${test.dir}/output">
>  
> Then, the tests are executed, but they still fail.
> 
> I will put the second issue in a second mail, otherwise it will become too confusing.
> 
> 
>> sessionInfo()
> R version 2.10.1 (2009-12-14) 
> x86_64-apple-darwin9.8.0 
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods  
> [8] base     
> 
> other attached packages:
> [1] RWebServices_1.10.0 TypeInfo_1.12.0     SJava_0.72.0       
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.3-1
>>
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793