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="${test.dir}/output"> + <jvmarg value="-Djava.library.path=/Library/Frameworks/R.framewor k/Resources/library/SJava/libs/x86_64/"/> <batchtest todir="${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 >

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/SJav a/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="${test.dir}/output"> > + <jvmarg value="-Djava.library.path=/Library/Frameworks/R.framew ork/Resources/library/SJava/libs/x86_64/"/> > <batchtest todir="${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 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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