[R] Problem with package SJava

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From: Nathan Whitehouse (nlwhitehouse@yahoo.com)
Date: Wed 19 May 2004 - 01:41:03 EST


Message-id: <20040518154103.84523.qmail@web12405.mail.yahoo.com>

Hi,

  This main method on class Essai will fail at least
for one reason becaue you need to instantiate a
ROmegahatInterpreter.
  
  Referencing this causes the R DLLs & the SJava DLLs
to load.
   However, it appears that they are already loaded,
judging from your output below based on the signal
11/Page fault error.

  Try adding it and seeing if it works. Can you get
it to work under linux?

  About the java compilation issue:
  
  you need to have the following jars in your
CLASSPATH

    $SJAVA_HOME/org/omegahat/Jars/jas.jar
    $SJAVA_HOME/org/omegahat/Jars/antlr.jar
    $SJAVA_HOME/org/omegahat/Jars/Environment.jar

  This might cause the compilation issue.

  Hope that is a little help. If you still have
problems, hopefully we can figure them out.

  Nathan

Hello all,
I'm trying to run SJava package (0.65 modified
downloaded from :
http://stats.math.uni-augsburg.de/iPlots/alpha/) on
windows NT 2000 and
R
1.8.01. I have also downloaded the PDF Calling R from
Java and when I
want
to execute the following code:
import org.omegahat.R.Java.*;
import java.io.*;
public class Essai{
        public static void main (String [] args) {
                REvaluator e = new REvaluator();
                Object val = e.eval("objects()");
                if (val!= null) {
                        String[] objects = (String[]) val;
                        for (int i = 0; i< objects.length; i++) {
                                System.out.println("("+i+") " + objects[i]);
                        }
                }
        }
}
I have in return:

An unexpected exception has been detected in native
code outside the
VM.
Unexpected Signal : EXCEPTION_ACCESS_VIOLATION
(0xc0000005) occurred at
PC=0x6B4B85E3
Function=R_SetMaxNSize+0xC3
Library=c:\Program Files\R\rw1081\bin\R.dll

Current Java thread:
        at org.omegahat.R.Java.REvaluator.eval(Native Method)
        at
org.omegahat.R.Java.REvaluator.eval(REvaluator.java:86)
        at
org.omegahat.R.Java.REvaluator.eval(REvaluator.java:36)
        at Toto.main(Toto.java:22)

Dynamic libraries:
0x00400000 - 0x00406000 C:\j2sdk1.4.2_03\bin\java.exe
0x78460000 - 0x784E3000 C:\WINNT\system32\ntdll.dll
0x78ED0000 - 0x78F32000
C:\WINNT\system32\ADVAPI32.dll
0x77E70000 - 0x77F33000
C:\WINNT\system32\KERNEL32.DLL
0x770C0000 - 0x77131000 C:\WINNT\system32\RPCRT4.DLL
0x78000000 - 0x78045000 C:\WINNT\system32\MSVCRT.dll
0x08000000 - 0x08138000
C:\j2sdk1.4.2_03\jre\bin\client\jvm.dll
0x77E00000 - 0x77E65000 C:\WINNT\system32\USER32.dll
0x77F40000 - 0x77F7E000 C:\WINNT\system32\GDI32.DLL
0x77540000 - 0x77571000 C:\WINNT\system32\WINMM.dll
0x10000000 - 0x10007000
C:\j2sdk1.4.2_03\jre\bin\hpi.dll
0x007C0000 - 0x007CE000
C:\j2sdk1.4.2_03\jre\bin\verify.dll
0x007D0000 - 0x007E9000
C:\j2sdk1.4.2_03\jre\bin\java.dll
0x007F0000 - 0x007FD000
C:\j2sdk1.4.2_03\jre\bin\zip.dll
0x18270000 - 0x18287000 C:\Program
Files\R\rw1081\library\SJava\libs\SJava.dll
0x6B400000 - 0x6B61B000 c:\Program
Files\R\rw1081\bin\R.dll
0x68180000 - 0x6819F000 c:\Program
Files\R\rw1081\bin\Rblas.dll
0x77B40000 - 0x77BC9000
C:\WINNT\system32\COMCTL32.DLL
0x76B00000 - 0x76B3E000
C:\WINNT\system32\COMDLG32.DLL
0x63180000 - 0x631C8000 C:\WINNT\system32\SHLWAPI.DLL
0x77580000 - 0x777CF000 C:\WINNT\system32\SHELL32.DLL
0x77810000 - 0x77817000 C:\WINNT\system32\VERSION.dll
0x75950000 - 0x75956000 C:\WINNT\system32\LZ32.DLL
0x77910000 - 0x77933000
C:\WINNT\system32\imagehlp.dll
0x72970000 - 0x7299D000 C:\WINNT\system32\DBGHELP.dll
0x68EA0000 - 0x68EAB000 C:\WINNT\system32\PSAPI.DLL

Heap at VM Abort:
Heap
  def new generation total 576K, used 227K
[0x10010000, 0x100b0000,
0x104f0000)
   eden space 512K, 44% used [0x10010000, 0x10048f68,
0x10090000)
   from space 64K, 0% used [0x10090000, 0x10090000,
0x100a0000)
   to space 64K, 0% used [0x100a0000, 0x100a0000,
0x100b0000)
  tenured generation total 1408K, used 0K
[0x104f0000, 0x10650000,
0x14010000)
    the space 1408K, 0% used [0x104f0000,
0x104f0000, 0x104f0200,
0x10650000)
  compacting perm gen total 4096K, used 1039K
[0x14010000, 0x14410000,
0x18010000)
    the space 4096K, 25% used [0x14010000,
0x14113de0, 0x14113e00,
0x14410000)

Local Time = Mon May 17 09:22:41 2004
Elapsed Time = 17
#
# The exception above was detected in native code
outside the VM
#
# Java VM: Java HotSpot(TM) Client VM (1.4.2_03-b02
mixed mode)
#

I try to recompile the native interfaces and I think
that some files or
directories are missing like:
antlr\commonAST.class
jas.classEnv

I don't know what I should do so I hope that anybody
could help me.
thanks,
Regards

Vincent

=====
Nathan Whitehouse
Statistics/Programming
Baylor College of Medicine
Houston, TX, USA
nlwhitehouse@yahoo.com
work: 1-713-798-9029
cell: 1-512-293-5840

http://rho-project.org: rho- open source web services for R.
http://franklin.imgen.bcm.tmc.edu: Shaw laboratory, bcm.

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