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

[Michael Dondrup]

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:

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
>