R devel - Apr 2009 - RJava question(class not found with rJava's vm, though found with alternate vm)

Not sure if this the right place, but I can't seem to subscribe to the rJava
mailing list. Sorry for the noise.

I have a jar file in the CLASSPATH variable. On running .jinit and checking
.jclassPath, i can see the jar file containing the class. Yet when trying to
instantaite the class, i get a class not found error.

Now If if, create my own vm (see below), and then run .jinit (which will use
my vm), i can find the class in question (org.apache.hadoop.io.longwritable)

Is there some classloader problem in rJava?

==code=void create_vm(const char *clap) {
  char* classpath = (char*) calloc(18+strlen(clap)+1, sizeof(char));
  sprintf(classpath,"-Djava.class.path=%s",clap);
  JavaVMInitArgs args;
  JavaVMOption options[2];
  args.version = JNI_VERSION_1_4;
  args.nOptions = 2;
  options[0].optionString = classpath;
  options[1].optionString = "-Xrs";
  args.options = options;
  args.ignoreUnrecognized = JNI_TRUE;
  JavaVM *jvms[32];
  jsize vms=0;
  int r=0;
  r=JNI_GetCreatedJavaVMs(jvms, 32, &vms);
  if (r) {
    error("JNI_GetCreatedJavaVMs returned %d\n", r);
  } else {
    if (vms>0) {
      int i=0;
      while (i<vms) {
    if (jvms[i]) {
      if (!(*jvms[i])->AttachCurrentThread(jvms[i], (void**)&jenv, NULL))
{
        jvm=jvms[i];
        break;
      }
    }
    i++;
      }
      if (i==vms) error("Failed to attach to any existing JVM.");
    }else {
        JNI_CreateJavaVM(&jvm, (void **)&jenv, &args);
      }
    }
  }


Saptarshi Guha

	[[alternative HTML version deleted]]

On Apr 5, 2009, at 9:26 AM, Saptarshi Guha wrote:
> Not sure if this the right place, but I can't seem to subscribe to  
> the rJava
> mailing list. Sorry for the noise.
>
The correct mailing list is stats-rosuda-devel:
http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel

(The rJava mailing list was a test but it turned out that everyone is  
still using stats-rosuda-devel so the idea of a separate list was  
abandoned).

> I have a jar file in the CLASSPATH variable. On running .jinit and  
> checking .jclassPath, i can see the jar file containing the class.  
> Yet when trying to instantaite the class, i get a class not found  
> error.
>
Can you, please, send me the exact code you're using? (I.e. exactly  
the value of CLASSPATH, your platform, how you started R and  
initialized rJava and what you tried to do to load the class).

A side note - preferably you should not be using the CLASSPATH  
environment variable, because that is very limited and doesn't work if  
you have multiple packages using Java. Instead use .jinit or .jpackage  
(under the hood CLASSPATH gets converted but that is for compatibility  
only).

> Now If if, create my own vm (see below), and then run .jinit (which  
> will use my vm), i can find the class in question  
> (org.apache.hadoop.io.longwritable)
>
> Is there some classloader problem in rJava?
>
No, more likely that your code is using the wrong class loader for  
loading files. The code below sets the path in the system class loader  
but that is not the loader used by R code. Since R needs to modify the  
class path on the fly (as packages are loaded) it uses its own class  
loader. It seems as if you are bypassing that loader and thus running  
into problems (without exact details we can't tell for sure).

Cheers,
Simon


> ==code=> void create_vm(const char *clap) {
>  char* classpath = (char*) calloc(18+strlen(clap)+1, sizeof(char));
>  sprintf(classpath,"-Djava.class.path=%s",clap);
>  JavaVMInitArgs args;
>  JavaVMOption options[2];
>  args.version = JNI_VERSION_1_4;
>  args.nOptions = 2;
>  options[0].optionString = classpath;
>  options[1].optionString = "-Xrs";
>  args.options = options;
>  args.ignoreUnrecognized = JNI_TRUE;
>  JavaVM *jvms[32];
>  jsize vms=0;
>  int r=0;
>  r=JNI_GetCreatedJavaVMs(jvms, 32, &vms);
>  if (r) {
>    error("JNI_GetCreatedJavaVMs returned %d\n", r);
>  } else {
>    if (vms>0) {
>      int i=0;
>      while (i<vms) {
>    if (jvms[i]) {
>      if (!(*jvms[i])->AttachCurrentThread(jvms[i], (void**)&jenv,  
> NULL)) {
>        jvm=jvms[i];
>        break;
>      }
>    }
>    i++;
>      }
>      if (i==vms) error("Failed to attach to any existing JVM.");
>    }else {
>        JNI_CreateJavaVM(&jvm, (void **)&jenv, &args);
>      }
>    }
>  }
>
>
> Saptarshi Guha
>
> 	[[alternative HTML version deleted]]
>
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