[R] unable to source a .R file using RJava

O'Brien, Laura lobrien at icoria.com
Wed Jul 27 18:42:58 CEST 2005 

I am unable to source a ".R" file using RJava.  I tried a couple of different tests:
     1)  using java and the evaluation method core dumps
     2)  using ./RJava --example --gui-none to invoke source core dumps. 
     3)  The line of R works if I go directly thru R and not RJava.

Version info and code are below. Any help would be appreciated.

--Laura O'Brien
Applications Architect



version info
------------
Java: 	j2sdk1.4.1_02
R: 		2.1.1
SJava:	0.68
OS:		SunOs 5.8


doNothing.R file I'd like to source
-----------------------------------

#
# $Author: lobrien $
#
# $Date: 2005/07/27 16:20:00 $
#
# $Header: /unixfiles/softengr/cvs/repository/hh/src/r/doNothing.R,v 1.2 2005/07/27 16:20:00 lobrien Exp $
#
#

#
# test file to see if I can source a .R file via SJava
#
# Works when
# ----------
#    I invoke R version 2.1.1 on SunOS jupiter 5.8
#  >  source ("/imports/nas1/people/lobrien/dist2.1_rc1/hh/src/r/doNothing.R")
#  >  res <- getData("something")
#  >  res
#  [1] 2
#
#
# doesn't work when
# -----------------
# (A)   launch R thru java via -->  ./RJava --example --gui-none
#       [omegahat->R] source ("/imports/nas1/people/lobrien/dist2.1_rc1/hh/src/r/doNothing.R")
#     
#       Unexpected Signal : 11 occurred at PC=0xFE0C2B44
#       Function=[Unknown.  Nearest:  JVM_Close+0x6BFC4]
#       <snip>
#
# (B)   call it via .java file.  See JavaRCall3



getData <- function(query,
                    db.name="csbdev",
                    user.name="noone",
                    passwd="pass"){
  R <- 2
  R
}

.java code to invoke the evaluate method
-----------------------------------------
package com.icoria.rwrapper;

import org.omegahat.R.Java.ROmegahatInterpreter;
import org.omegahat.R.Java.REvaluator;


public class JavaRCall3
{

    /**
     * want to see if I can eval a t.test command like what I would run in the
     * R command line
     */

    static public void run_sourceRFile(REvaluator e, ROmegahatInterpreter interp)
    {
        /* produces a core */
        System.err.println("running source doNothing.R");

        Object value = e.eval("source (\"/imports/nas1/people/lobrien/dist2.1_rc1/hh/src/r/doNothing.R");
        if (value != null)
            interp.show(value);
    }


   
    
    /**
     * 
     */
    static public void main(String[] args) 
    {
        ROmegahatInterpreter interp = new ROmegahatInterpreter(ROmegahatInterpreter.fixArgs(args), false);
        REvaluator e = new REvaluator();

        Object[] funArgs;
        String[] objects;
        Object value;
        int i;

        run_sourceRFile(e, interp);   
    }
}

the corresponding core dump when using java
--------------------------------------------
[lobrien at fox] ./RJava
Loading RInterpreter library

R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.

running source doNothing.R
Problems: unrecognized user-level object of mode 0
Error: No default Java type for S class ???

An unexpected exception has been detected in native code outside the VM.
Unexpected Signal : 11 occurred at PC=0xF1835E50
Function=setup_Rmainloop+0x4F8
Library=/imports/filer04/tools/app/R-2.1.1/lib/R/lib/libR.so

Current Java thread:
        at org.omegahat.R.Java.REvaluator.eval(Native Method)
        at org.omegahat.R.Java.REvaluator.eval(REvaluator.java:90)
        at org.omegahat.R.Java.REvaluator.eval(REvaluator.java:40)
        at com.icoria.rwrapper.JavaRCall3.run_sourceRFile(JavaRCall3.java:25)
        at com.icoria.rwrapper.JavaRCall3.main(JavaRCall3.java:46

Dynamic libraries:
0x10000         /tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/bin/java
0xff360000      /usr/lib/libthread.so.1
0xff3a0000      /usr/lib/libdl.so.1
0xff200000      /usr/lib/libc.so.1
0xff330000      /usr/platform/SUNW,Ultra-60/lib/libc_psr.so.1
0xfe000000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/client/libjvm.so
0xff2d0000      /usr/lib/libCrun.so.1
0xff1e0000      /usr/lib/libsocket.so.1
0xff100000      /usr/lib/libnsl.so.1
0xff0d0000      /usr/lib/libm.so.1
0xff300000      /usr/lib/libw.so.1
0xff0b0000      /usr/lib/libmp.so.2
0xff080000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/native_threads/libhpi.so
0xff050000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/libverify.so
0xfe7c0000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/libjava.so
0xff020000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/libzip.so
0xfdfc0000      /imports/filer04/tools/app/R-2.1.1/lib/R/library/SJava/libs/SJava.so
0xfdf90000      /imports/filer04/tools/app/R-2.1.1/lib/R/library/SJava/libs/libRSNativeJava.so
0xf1780000      /imports/filer04/tools/app/R-2.1.1/lib/R/lib/libR.so
0xfc7c0000      /tools/app/gcc-3.4.3/lib/libg2c.so.0
0xfc4e0000      /tools/app/gcc-3.4.3/lib/libgcc_s.so.1
0xfc4b0000      /tools/app/R-2.1.1/lib/R/library/grDevices/libs/grDevices.so
0xfc450000      /tools/app/R-2.1.1/lib/R/library/stats/libs/stats.so
0xfc430000      /tools/app/R-2.1.1/lib/R/library/methods/libs/methods.so

Local Time = Wed Jul 27 12:37:24 2005
Elapsed Time = 5
#
# The exception above was detected in native code outside the VM
#
# Java VM: Java HotSpot(TM) Client VM (1.4.1_02-b06 mixed mode)
#
# An error report file has been saved as /tmp/hs_err_pid22533.log.
# Please refer to the file for further information.
#
Abort

using ./RJava --example --gui-none to invoke source core dumps. 
---------------------------------------------------------------
[omegahat->R] source ("/imports/nas1/people/lobrien/dist2.1_rc1/hh/src/r/doNothing.R")

Unexpected Signal : 11 occurred at PC=0xFE0C2B44
Function=[Unknown. Nearest: JVM_Close+0x6BFC4]
Library=/imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/client/libjvm.so

Current Java thread:
        at org.omegahat.R.Java.REvaluator.eval(Native Method)
        at org.omegahat.R.Java.REvaluator.eval(REvaluator.java:90)
        at org.omegahat.R.Java.REvaluator.eval(REvaluator.java:40)
        at org.omegahat.R.Java.Examples.JavaRPrompt.main(JavaRPrompt.java:26)

Dynamic libraries:
0x10000         /tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/bin/java
0xff360000      /usr/lib/libthread.so.1
0xff3a0000      /usr/lib/libdl.so.1
0xff200000      /usr/lib/libc.so.1
0xff330000      /usr/platform/SUNW,Ultra-60/lib/libc_psr.so.1
0xfe000000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/client/libjvm.so
0xff2d0000      /usr/lib/libCrun.so.1
0xff1e0000      /usr/lib/libsocket.so.1
0xff100000      /usr/lib/libnsl.so.1
0xff0d0000      /usr/lib/libm.so.1
0xff300000      /usr/lib/libw.so.1
0xff0b0000      /usr/lib/libmp.so.2
0xff080000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/native_threads/libhpi.so
0xff050000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/libverify.so
0xfe7c0000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/libjava.so
0xff020000      /imports/filer04/tools/app/j2sdk1.4.1_02-20030305/j2sdk1.4.1_02/jre/lib/sparc/libzip.so
0xfdfc0000      /imports/filer04/tools/app/R-2.1.1/lib/R/library/SJava/libs/SJava.so
0xf1780000      /imports/filer04/tools/app/R-2.1.1/lib/R/lib/libR.so
0xfc7c0000      /tools/app/gcc-3.4.3/lib/libg2c.so.0
0xfc4e0000      /tools/app/gcc-3.4.3/lib/libgcc_s.so.1
0xfc4b0000      /tools/app/R-2.1.1/lib/R/library/grDevices/libs/grDevices.so
0xfc450000      /tools/app/R-2.1.1/lib/R/library/stats/libs/stats.so
0xfc430000      /tools/app/R-2.1.1/lib/R/library/methods/libs/methods.so
0xfa3c0000      /tools/app/R-2.1.1/lib/R/modules/R_X11.so
0xfc410000      /usr/lib/libSM.so.6
0xfa390000      /usr/lib/libICE.so.6
0xf1680000      /usr/lib/libX11.so.4
0xfa2d0000      /usr/lib/libXext.so.0

Local Time = Wed Jul 27 12:39:30 2005
Elapsed Time = 37
#
# HotSpot Virtual Machine Error : 11
# Error ID : 4F530E43505002E6 01
# Please report this error at
# http://java.sun.com/cgi-bin/bugreport.cgi
#
# Java VM: Java HotSpot(TM) Client VM (1.4.1_02-b06 mixed mode)
#
# An error report file has been saved as /tmp/hs_err_pid22537.log.
# Please refer to the file for further information.
#
Abort

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