Can not handle R results due to : rcaller.exception.RCallerParseException: Can not parse the R output: org.xml.sax.SAXParseException: Premature end of file

GoogleCodeExporter commented 8 years ago

What steps will reproduce the problem?

caller.addDoubleArray("x", x);
caller.addDoubleArray("y", y);
caller.addRCode("ols<-lm(y~x)");
caller.runAndReturnResult("ols");

What is the expected output? What do you see instead?
Throws exception defined in the subject.

Please use labels and text to provide additional information.

Original issue reported on code.google.com by mhsatman on 22 Jul 2011 at 8:10

GoogleCodeExporter commented 8 years ago

Solved.

Original comment by mhsatman on 27 Jul 2011 at 7:27

GoogleCodeExporter commented 8 years ago

Hello,

   I just installed RCaller and got the same exact exception behavior above. What is the solution ??

Thanks!

Original comment by alejandr...@gmail.com on 13 Sep 2011 at 5:15

GoogleCodeExporter commented 8 years ago

can you please post your code and complete error tree?

Original comment by mhsatman on 14 Sep 2011 at 12:26

GoogleCodeExporter commented 8 years ago

As a user reported, after installing the package Runiversal, he has no longer 
had the same error. In R type

install.packages("Runiversal")

manually and run your class again. This package should be installed and loaded 
automatically by the RCaller but it is not realized as supposed in Windows 
systems.

Original comment by mhsatman on 30 Sep 2011 at 7:06

GoogleCodeExporter commented 8 years ago

Your suggestion solves the problem for the time being.

However, R installs packages in a temporary directory, so the problem could 
resurface any time. Is there a more permanent solution on the way?

Also, may I suggest documenting this in a wiki pages, so it's more obvious to 
new users?

Original comment by ursreu...@gmail.com on 11 Oct 2011 at 10:01

GoogleCodeExporter commented 8 years ago

It seems the Runiversal package must be installed by an external way but I will 
consider your suggestion for this.

Would you want to join project for editing wiki and the code?

Original comment by mhsatman on 11 Oct 2011 at 10:17

GoogleCodeExporter commented 8 years ago

If you are alright with not much happening on my side once this is done, I'll 
do it.
My interest in R is temporary at best, because right now, it's the easiest way 
to solve a problem at work.

Just drop me a message if you decide to add me anyway.

Original comment by ursreu...@gmail.com on 12 Oct 2011 at 9:27

GoogleCodeExporter commented 8 years ago

import java.io.File;
import javax.swing.ImageIcon;
import rcaller.RCaller;

public class Test1 {

    public static void main(String[] args) {
        new Test1();
    }

    /*
     * Test for simple plots
     */
    public Test1() {
        try {
            RCaller caller = new RCaller();
            caller.setRscriptExecutable("/usr/bin/Rscript");
            caller.cleanRCode();

            double[] numbers = new double[]{1, 4, 3, 5, 6, 10};

            caller.addDoubleArray("x", numbers);
            caller.addRCode("my.mean<-mean(x)");
            caller.runAndReturnResult("my.mean");

            double[] result;

            result = caller.getParser().getAsDoubleArray("mean");
            System.out.println("Mean is "+result[0]);

        } catch (Exception e) {
            System.out.println(e.toString());
        }
    }
}

** This is my code and getting the above error.

I had already installed Runiversal
its located in /tmp/RtmpobLsMT/downloaded_packages

Original comment by vinnida...@gmail.com on 15 Dec 2011 at 9:08

GoogleCodeExporter commented 8 years ago

change your code to

 double[] numbers = new double[]{1, 4, 3, 5, 6, 10};

            caller.addDoubleArray("x", numbers);
            caller.addRCode("results<-list(mymean = mean(x))");
            caller.runAndReturnResult("results");

            double[] result;

            result = caller.getParser().getAsDoubleArray("mymean");

Original comment by mhsatman on 15 Dec 2011 at 9:46

GoogleCodeExporter commented 8 years ago

Its still not working..
I am sending error and .java file.
please have a look.

thanks..

Original comment by vinnida...@gmail.com on 15 Dec 2011 at 12:27

Attachments:

GoogleCodeExporter commented 8 years ago

your code is ok. it should run. Please, check the path of Rscript and correct 
if it is not in /usr/bin

Original comment by mhsatman on 16 Dec 2011 at 7:18

GoogleCodeExporter commented 8 years ago

No the path is fine..
I'd started with R installing 2.14.0 version but was unable to install 
Runiversal, thus i installed r 2.13.2 version without uninstalling the previous 
one 
May this be a problem..
Or there may be some problem with path of Runiversal installed.

Thanks
vin

Original comment by vinnida...@gmail.com on 17 Dec 2011 at 8:04

GoogleCodeExporter commented 8 years ago

Solved!!

the path of Rscript that worked was in the bin dir of R installed...
and I was trying that of /usr/bin of Ubuntu...

Thanks a lot..
- vin

Original comment by vinnida...@gmail.com on 17 Dec 2011 at 10:02

GoogleCodeExporter commented 8 years ago

I got the same error. I'm running R on mac, and installed Runiversal already. 
Here's my code:

            Random random = new Random();
            RCaller caller = new RCaller();

            caller.setRscriptExecutable("/usr/bin/Rscript");

            double[] data = new double[100];
            for (int i = 0; i < data.length; i++) {
                data[i] = random.nextGaussian();
            }

            caller.addDoubleArray("x", data);

            caller.addRCode("my.model <- arima(x,order=c(1,1,1))");
            caller.addRCode("my.pd <- options(digits=5)");

            caller.addRCode("results<-list(pred=predict(model))");

            caller.runAndReturnResult("results");

            double[] results;

            results = caller.getParser().getAsDoubleArray("pred");
            System.out.println("prediction is " + results[0]);

Original comment by yangsun....@gmail.com on 7 Feb 2012 at 12:02

GoogleCodeExporter commented 8 years ago

Thank you all for sharing the issues.

I also got the same problem and the same error.
Any progress fixing. I tried to figured it inside out with
- change of path
- change of R version

Nothing worked so far... 

al

Original comment by apptvieu...@gmail.com on 24 Feb 2012 at 8:52

GoogleCodeExporter commented 8 years ago

I got same problem. but I solved by set 'BOTH' correct RExecutable and 
RscriptExecutable path.

Original comment by manmustb...@gmail.com on 30 Mar 2012 at 5:38

GoogleCodeExporter commented 8 years ago

I got same problem too.

..................
 caller.setRscriptExecutable("C:/Program Files/R/bin/Rscript.exe");

code.addRCode("ausgangsstoff <- 200.0");
code.addRCode("k.eins <- 5");
code.addRCode("k.zwei <- 8");
code.addRCode("k.drei <- 7");
code.addRCode("zeit <- seq(,12, by=0.01)");
code.addRCode("c.drei <- rep(NA, length(zeit)");
code.addRCode("for(i in 1:length(zeit)){c.drei[i] = 
ausgangsstoff*((k.zwei/(k.eins-k.zwei-k.drei))*exp(-k.eins*zeit[i])-(k.eins*k.zw
ei/((k.eins-k.zwei-k.drei)*(k.zwei*k.drei)))*exp(-1*(k.zwei+k.drei)*zeit[i])+k.z
wei/(k.zwei+k.drei))}");

code.addRCode("results<-list(test=c.drei)");

caller.setRCode(code);
caller.runAndReturnResult("results");
...............
the Rscript path is correct and i have install the lates Version of R..But what 
is the problem now? can anybody help?

Original comment by Stefan.K...@gmail.com on 2 Apr 2012 at 6:09

GoogleCodeExporter commented 8 years ago

The way I solved it: (I'm using 64 bit version of R), so in the code I just 
changed the line: 
caller.setRscriptExecutable("C:/Program Files/R/R-2.15.0/bin/Rscript");
to the following line:
caller.setRscriptExecutable("C:/Program Files/R/R-2.15.0/bin/x64/Rscript");

(please note that I'm using RCaller-2.0.7.jar as source). it's attached

Original comment by ro...@anametrix.com on 7 Apr 2012 at 1:22

GoogleCodeExporter commented 8 years ago

i have try it with the same R version but with RCaller 2.1.0 and it doesnt work 
i dont know why the sample application on the RCaller Site works but not my 
example

Original comment by Stefan.K...@gmail.com on 7 Apr 2012 at 6:42

GoogleCodeExporter commented 8 years ago

[deleted comment]

GoogleCodeExporter commented 8 years ago

YIPPI i found the error it works now
look here is my error
code.addRCode("c.drei <- rep(NA, length(zeit)");

one round bracket is missing correct is
code.addRCode("c.drei <- rep(NA, length(zeit))");

Original comment by Stefan.K...@gmail.com on 8 Apr 2012 at 9:36

GoogleCodeExporter commented 8 years ago

[deleted comment]

GoogleCodeExporter commented 8 years ago

Hi, I have try to run the Rcaller in my java program. I got some error when i 
was import r packages inside the java code using RCaller library. Please let me 
know the solution to solve this problem. This is my sample code given below.

            RCaller caller = new RCaller();
            caller.setRscriptExecutable("/usr/local/bin/Rscript");
            caller.cleanRCode();

            String[] data = new String[]{"test","test1" , "test3", "test4", "test5", "test6"};

            caller.addStringArray("x", data);
            caller.R_require("tm");
            caller.addRCode("text<-paste(x)");
            caller.addRCode("cp<-Corpus(text)");
            caller.runAndReturnResult("cp");

            String[] result;

            result = caller.getParser().getAsStringArray("cp");
            System.out.println("Text is "+result[0]);

My error message is : 

[Fatal Error] Routput4733190479360896857:1:1: Premature end of file.
require(tm)
packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org"
}

packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org"
}

x<-c("test", "test1", "test3", "test4", "test5", "test6");
my.mean<-c(x)
cp<-corpus(my.mean)
cat(makexml(obj=cp, name="cp"), file="/tmp/Routput4733190479360896857")

rcaller.exception.RCallerExecutionException: Can not handle R results due to : 
rcaller.exception.RCallerParseException: Can not parse the R output: 
org.xml.sax.SAXParseException: Premature end of file.

Original comment by zimbh...@gmail.com on 12 Apr 2012 at 7:39

GoogleCodeExporter commented 8 years ago

Copy and paste your generated r code into the r interpreter and see what is the 
error with your code.

Original comment by mhsatman on 12 Apr 2012 at 7:41

GoogleCodeExporter commented 8 years ago

Hello,

Rcaller seems to work pretty well and I am starting to use it as I want to have 
my scripts written in R and run them from Java.

I am having the exact same problem with this exception.

For a first test, I generated R code to create a pdf file and call it from 
java. It is something easy, and worked fine, the pdf file was generated 
properly.
Now, I want to call again one “.R file” containing a particular function 
within, but the problem is always the same:

[Fatal Error] Routput4280160344587065721:1:1: Premature end of file.
packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org")
}
packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org")
}
cat(makexml(obj=ols, name="ols"), 
file="C:/DOCUME~1/MBMONT~1/CONFIG~1/Temp/Routput8192804637477966385")
source("C:/Documents and Settings/mbmonteiro/Escritorio/Cima/Java_test.R")
q("yes")
source("C:/Documents and Settings/mbmonteiro/Escritorio/Cima/Java_test_2.R")
q("yes")
set.seed(1234)
x <- rpois(500, 4)
y <- mysummary(x)
cat(makexml(obj=y, name="y"), 
file="C:/DOCUME~1/MBMONT~1/CONFIG~1/Temp/Routput4280160344587065721")

rcaller.exception.RCallerExecutionException: Can not handle R results due to : 
rcaller.exception.RCallerParseException: Can not parse the R output: 
org.xml.sax.SAXParseException; systemId: 
file:/C:/DOCUME~1/MBMONT~1/CONFIG~1/Temp/Routput4280160344587065721; 
lineNumber: 1; columnNumber: 1; Premature end of file.

I know I have the correct RScript path  
caller.setRscriptExecutable("C:/Archivos de programa/R/R-2.15.0/bin/Rscript");
and that “Runiversal” is installed.
I also tested to call it from the R console source("C:/Documents and 
Settings/mbmonteiro/Escritorio/Cima/Java_test_2.R") and I could use mysummary 
function properly.
Could someone help me to understand how should I call a function from the file 
and use its parameters from java.

CODE that is giving problems:
caller.addRCode("source(\"C:/Documents and 
Settings/mbmonteiro/Escritorio/Cima/Java_test_2.R\")");
caller.runOnly();
caller.addRCode("set.seed(1234)");
caller.addRCode("x <- rpois(500, 4)");
caller.addRCode("y <- mysummary(x)");
caller.runAndReturnResult("y");

Please find the entire java code attached.

I am looking forward to hearing from you,
Mariana

Original comment by marianab...@gmail.com on 20 Sep 2012 at 10:22

Attachments:

Java_code.txt

GoogleCodeExporter commented 8 years ago

Hello,
Thank you for your RCaller library.
Here is my R code which is working:

> file.choose()
[1] "/Users/bendarraz/Documents/ObjTable.RData"
> file<-file.choose()
> load(file)
> seed.landslide <- sample(ObjTable$Mean.OID[(which(ObjTable$class_name == 
'landslide'))], 1)     
> seed.non.landslide <- sample(ObjTable$Mean.OID[(which(ObjTable$class_name == 
'non landslide'))], 1)
> selection <- c(seed.landslide, seed.non.landslide)
> selection
[1]  56736 105804
> new.OID <- query(ObjTable, selection, n.trees=50)
> new.OID
[1] 301848

I got the same error. I'm running R on mac, and installed Runiversal already. 
Here's my Java code:

                      caller.setRscriptExecutable("/usr/bin/Rscript");
              String file = "/Users/bendarraz/Documents/ObjTable.RData"; 
              /*
               * Adding R Code
               */
              code.addRCode("load(file)");
              code.addRCode("seed.landslide <- sample(ObjTable$Mean.OID[(which(ObjTable$class_name == 'landslide'))], 1)");
              code.addRCode("seed.non.landslide <- sample(ObjTable$Mean.OID[(which(ObjTable$class_name == 'non landslide'))], 1)");
              code.addRCode("selection <- c(seed.landslide, seed.non.landslide)");  
                      code.addRCode ("source(/Users/bendarraz/Documents/query.r)");
                      code.addRCode("nouveau.OID <- query(ObjTable, selection, n.trees=50)");
                      double[] results;

              results = caller.getParser().getAsDoubleArray("nouveau.OID");

              System.out.println("nouveau.OID" + results[0]);

I use both external objTable.Rdata and query.R files. 
I would like to display the results but it seems that the runAndReturnResult() 
and getAsDoubleArray() methods don't work in this case.

I tried several solutions found in these comments (path of Rscript, using 
"list()" instead of "new.OID", installing Runiversal...) without success.

Thank you for helping.

Best regards.

Original comment by bendar...@gmail.com on 21 Sep 2012 at 9:33

GoogleCodeExporter commented 8 years ago

2 questions:

Is it correct to call an Rdata file like this:
code.R_source("/Users/bendarraz/Documents/ObjTable.RData");

Is it legal to write like in R a statement like this with Rcaller?
code.addRCode("seed.landslide <- 
sample(ObjTable$Mean.OID[(which(ObjTable$class_name == 'landslide'))], 1)");

Thanks

Original comment by bendar...@gmail.com on 2 Oct 2012 at 8:32

GoogleCodeExporter commented 8 years ago

Juste a preciseness: the R_source is not indicated for Rdata files.

But my load statement doesn't work anyway:
code.addRCode("load(/Users/bendarraz/Documents/ObjTable.RData)");

Any idea about how to fix my issue?

Thank you

Original comment by bendar...@gmail.com on 3 Oct 2012 at 8:58

GoogleCodeExporter commented 8 years ago

Hello
I'm trying RCaller in order to execute BG-NBD analysis
I downloaded this jar "RCaller-2.1.1-SNAPSHOT.jar" and I tried to execute the R 
code listed on this url: http://code.google.com/p/clv-master-thesis/. I need to 
use this R code: 
http://code.google.com/p/clv-master-thesis/source/browse/trunk/model-bg-nbd.R
Now I installed the Runiversal package and I tried this sample:
              RCaller caller = new RCaller();
//            caller.setRscriptExecutable("/usr/bin/Rscript");
              caller.setRscriptExecutable("/usr/bin/Rscript");
              RCode code = new RCode();
              code.clear();

              double[] numbers = new double[]{1, 4, 3, 5, 6, 10};

              code.addDoubleArray("x", numbers);
              File file = code.startPlot();
              System.out.println("Plot will be saved to : " + file);
              code.addRCode("plot.ts(x)");
              code.endPlot();

              caller.setRCode(code);
              caller.runOnly();
              code.showPlot(file);
All works pretty good
I wanted to adapt it to my scenario and I wrote this unit test:
            //Installare R sulla macchina e poi il package RUniversal
            InputStreamReader reader = new InputStreamReader(Thread.currentThread().getContextClassLoader().getResourceAsStream("model-bg-nbd.R"));
            BufferedReader br = new BufferedReader(reader);
            String line = null;
            RCaller caller = new RCaller();
            //Punto allo script R (file chiamato 'R')
            caller.setRscriptExecutable("/usr/bin/Rscript");
            //Inizializzo tutto
            caller.cleanRCode();
            RCode code = new RCode();
            code.clear();
            int dimensione = 5;
            List<String> datas = new ArrayList<String>(dimensione);
            String dataFrameElement = null;
            for(int i = 0; i < dimensione; i++){
                if( i == 0 ){
                    dataFrameElement = "ID Tempo Utente Test";
                }else{
                    dataFrameElement = Math.random()*100+" "+Math.random()*100+" "+Math.random()*100+" "+Math.random()*100;
                }
                datas.add(dataFrameElement);
            }
            code.addStringArray("data", datas.toArray(new String[datas.size()]));
            while( (line = br.readLine()) != null ){

                //Aggiungo solo codice che non sia un commento
                if(!line.startsWith("#")){

                    code.addRCode(line);
                }
            }
            String doMle = "mle<-bgEstimateParameters(data, list(r=1, alpha=2, a=1, b=2));";
            code.addRCode(doMle);
            caller.setRCode(code);
            caller.runAndReturnResult("mle");
            String[] results = caller.getParser().getAsStringArray("mle");
            logger.info(results[0]);
        } catch (Exception e) {

            logger.error(e.getMessage(), e);
        }

When I execute it I get this error:
packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org")
}

data<-c("ID Tempo Utente Test", "56.38316672941737 3.9741386375765853 
57.82223487749921 52.82761425632678", "44.36318489079512 71.01945017181191 
77.46259908894473 0.3534156420011203", "20.681228545078902 66.41194421149585 
73.24614746149979 43.37634970010023", "92.28649039744393 30.800014223302007 
41.60373846010842 91.87173373444988");

bgLlh <- function(data, r, alpha, a, b) {
  with (data, {
    if (a<=0 | b<=0 | r<=0 | alpha<=0) return (NaN)
    term1 <- ( gamma(r+x) * alpha^r ) / gamma(r)
    term2 <- ( gamma(a+b) * gamma(b+x) ) / (gamma(b) * gamma(a+b+x))
    term3 <- 1
    term4 <- (1/(alpha + T))^(r+x)
    term5 <- (a/(b+x-1)) * (1/(alpha + tx))^(r+x)
    llh <- log(term1) + log(term2) + log(term3) + log(term4 + as.numeric(x>0)*term5)
    f <- -sum(llh)
    return (f)
  })
}

bgEstimateParameters <- function(data, initValues, safeMode=FALSE) {
  llhd <- function(r, alpha, a, b) {
    return (bgLlh(data, r, alpha, a, b))
  }
  library(bbmle)
  if (safeMode) {
    fit <- mle2(llhd, initValues, skip.hessian=TRUE, method="Nelder-Mead")
  } else {
    fit <- mle2(llhd, initValues)
  }
  return (fit)
}

bgComputePActive <- function(data, params) {
  if (class(params)[1] == "mle2") params <- as.list(coef(params))
  with (c(data,params), {
    term1 <- (a / (b + x - 1)) * ((alpha+T)/(alpha+tx))^(r+x)
    return (1 / (1 + as.numeric(x>0)*term1))
  })
}

bgPx <- function(t,x,params) {
  with(params, {
    term1 <- (beta(a,b+x)/beta(a,b))*(gamma(r+x)/(gamma(r)*factorial(x)))*(alpha/(alpha+t))^r*(t/(alpha+t))^x
    if (x==0) {
      term2 <- 0
    } else {
      seq <- 0:(x-1)
      term2a <- (gamma(r+seq)/(gamma(r)*factorial(seq)))*(t/(alpha+t))^seq
      term2 <- (beta(a+1,b+x-1)/beta(a,b))*(1-(alpha/(alpha+t))^r*sum(term2a))
    }
    return (term1+term2)
  })
}

bgConditionalForecast <- function(data, params, t) {
  if (class(params)[1] == "mle2") params <- as.list(coef(params))
  with(c(data,params), {
    term1 <- ((a+b+x-1)/(a-1))
    term2 <- 1-((alpha+T)/(alpha+T+t))^(r+x)*h2f1(r+x,b+x,a+b+x-1,t/(alpha+T+t))
    term3 <- 1 + as.numeric(x>0)*(a/(b+x-1))*((alpha+T)/(alpha+tx))^(r+x)
    # TODO: 1/term3 = PActive !?
    out <- term1 * term2 / term3
    return (out)
  })
}
mle<-bgEstimateParameters(data, list(r=1, alpha=2, a=1, b=2));
cat(makexml(obj=mle, name="mle"), file="/tmp/Routput359342344387748448")

13:30:23,228 ERROR [TestScriptingLanguagesCalling] Can not handle R results due 
to : rcaller.exception.ParseException: Can not parse output: The generated file 
/tmp/Routput359342344387748448 is empty
rcaller.exception.ParseException: Can not handle R results due to : 
rcaller.exception.ParseException: Can not parse output: The generated file 
/tmp/Routput359342344387748448 is empty
    at rcaller.RCaller.runAndReturnResult(RCaller.java:412)
    at it.eng.test.TestScriptingLanguagesCalling.testRCaller(TestScriptingLanguagesCalling.java:95)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:44)
    at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:15)
    at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:41)
    at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:20)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:76)
    at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
    at org.junit.runners.ParentRunner$3.run(ParentRunner.java:193)
    at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:52)
    at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:191)
    at org.junit.runners.ParentRunner.access$000(ParentRunner.java:42)
    at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:184)
    at org.junit.runners.ParentRunner.run(ParentRunner.java:236)
    at org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:50)
    at org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:467)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:683)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:390)
    at org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:197)

I can't figure what I'm wrong.
Can you give me any tips?

Cheers,
Angelo

Original comment by angelo...@gmail.com on 20 Nov 2012 at 12:31

GoogleCodeExporter commented 8 years ago

Hi there...any news about the showed error?

Original comment by angelo...@gmail.com on 21 Nov 2012 at 8:29

GoogleCodeExporter commented 8 years ago

Hai,

    I am trying to read the protein sequences from online biologiclal DB. The code works well in R. Now i want to execute R script via Java. But i got error. please help....

My Code:

import rcaller.RCaller;  
import rcaller.RCode;
public class ReadSeq
{
    public ReadSeq()
    {
     try
        {
            RCaller caller = new RCaller();
            RCode code=new RCode();
            code.clear();
            caller.setRscriptExecutable("C:\\Program Files\\Option\\R-2.15.1\\bin\\RScript.exe"); 
            code.addRCode("library(\"seqinr\")");
            code.addRCode("retrieveseqs <- function(seqnames,acnucdb)");
            code.addRCode("{");
            code.addRCode("myseqs <- list()");
            code.addRCode("require(\"seqinr\")");
            code.addRCode("choosebank(acnucdb)");
            code.addRCode("for (i in 1:length(seqnames))");
            code.addRCode("{");
            code.addRCode("seqname <- seqnames[i]");
            code.addRCode("print(paste(\"Retrieving sequence\",seqname,\"...\"))");
            code.addRCode("queryname <- \"query2\"");
            code.addRCode("query <- paste(\"AC=\",seqname,sep=\"\")");
            code.addRCode("query(`queryname`,`query`)");
            code.addRCode("seq <- getSequence(query2$req[[1]])");
            code.addRCode("myseqs[[i]] <- seq");
            code.addRCode("}");
            code.addRCode("closebank()");
            code.addRCode("return(myseqs)");
            code.addRCode(" }");
            code.addRCode("seqnames <- c(\"ACY70669\",\"ACQ44515\",\"Q6YMS4\",\"Q58HT7\")");
            code.addRCode("seqs <- retrieveseqs(seqnames,\"swissprot\")");
            code.addRCode("write.fasta(seqs, seqnames, file=\"type.fasta\"");
            caller.setRCode(code);
            //caller.runOnly();
            caller.runAndReturnResult("seqs");
           // System.out.println(caller.getParser().getXMLFileAsString());
            //String[] s=new String[10]; 
            //s=
            //System.out.println("hai");

            //System.out.println(s[0]);
            String[] v = caller.getParser().getAsStringArray("seqs");     
            for (int i = 0; i < v.length; i++)
            {         
                System.out.println(v[i]);        
            }
         }
        catch (Exception e){
            System.out.println(e.toString());
            }
        }
     public static void main(String args[])
     {
         ReadSeq R=new ReadSeq();
     }
    }

Error i got:
[Fatal Error] Routput3632:1:1: Premature end of file.
packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org")
}

library("seqinr")
retrieveseqs <- function(seqnames,acnucdb)
{
myseqs <- list()
require("seqinr")
choosebank(acnucdb)
for (i in 1:length(seqnames))
{
seqname <- seqnames[i]
print(paste("Retrieving sequence",seqname,"..."))
queryname <- "query2"
query <- paste("AC=",seqname,sep="")
query(`queryname`,`query`)
seq <- getSequence(query2$req[[1]])
myseqs[[i]] <- seq
}
closebank()
return(myseqs)
 }
seqnames <- c("ACY70669","ACQ44515","Q6YMS4","Q58HT7")
seqs <- retrieveseqs(seqnames,"swissprot")
write.fasta(seqs, seqnames, file="type.fasta"
cat(makexml(obj=seqs, name="seqs"), 
file="C:/Users/PRINCI~1/AppData/Local/Temp/Routput3632")//This file is Empty

rcaller.exception.RCallerExecutionException: Can not handle R results due to : 
rcaller.exception.RCallerParseException: Can not parse the R output: 
org.xml.sax.SAXParseException: Premature end of file.

Original comment by aruna23j...@gmail.com on 9 Jan 2013 at 6:20

GoogleCodeExporter commented 8 years ago

Please have a look at my code & error and give me a suggestion....
Thank You

Original comment by aruna23j...@gmail.com on 10 Jan 2013 at 6:27

GoogleCodeExporter commented 8 years ago

I googled for hours but cant find a solution Please help me....

Original comment by aruna23j...@gmail.com on 18 Jan 2013 at 5:32

GoogleCodeExporter commented 8 years ago

Hello,

I think that this article handle the problem of "Premature end of file". I'm 
not a developper, but I think that you will understand how to solve it : 
http://www.danielschneller.com/2008/01/saxparseexception-1-1-premature-end-of.ht
ml

This is not a tip for the end user but an insight to the developper (or any one 
who wish to help) to resolve the problem.

Original comment by hammami....@gmail.com on 11 Apr 2013 at 4:10

GoogleCodeExporter commented 8 years ago

[deleted comment]

GoogleCodeExporter commented 8 years ago

Hello,

I am writing program using RCaller 2.1.1-SNAPSHOT. Problem is when i use code 
from external library it says Routput file is empty. Here is my code:

      Random random = new Random();

      RCaller caller = new RCaller();
      RCode code = new RCode();

      caller.setRscriptExecutable("C:/Program Files/R/R-2.14.2/bin/x64/Rscript.exe");

      double[] data = new double[100];

      for (int i = 0; i < data.length; i++) {
        data[i] = random.nextGaussian();
      }

      code.addDoubleArray("x", data);

      code.addRCode("setwd('C:/Radek/')");
      code.addRCode("wd=list.files()");
      code.addRCode("library(Biobase)");
      //code.addRCode("targets=read.AnnotatedDataFrame('targets.txt',row.names=1,as.is=TRUE)");// WHEN I USE THIS IT CRASH
      code.addRCode("my.mean<-mean(x)");
      code.addRCode("my.var<-var(x)");
      code.addRCode("my.sd<-sd(x)");
      code.addRCode("my.min<-min(x)");
      code.addRCode("my.max<-max(x)");
      code.addRCode("my.standardized<-scale(x)");

      code.addRCode(
              "my.all<-list(mean=my.mean, variance=my.var, sd=my.sd, min=my.min, max=my.max, std=my.standardized)");
      caller.setRCode(code);
      caller.runAndReturnResult("wd");

      String[] results;
      results = caller.getParser().getAsStringArray("wd");
      System.out.println("Mean is " + results[0]);

Original comment by Bartek22...@gmail.com on 29 May 2013 at 3:02

GoogleCodeExporter commented 8 years ago

"#31 aruna23j...@gmail.com"

I have known how to solve your problem .you have to install the  "Runiversal" 
Package at first.

Original comment by hkp...@gmail.com on 8 Jul 2013 at 6:05

GoogleCodeExporter commented 8 years ago

Hello,
I have a problem with Rcalling.
I work with R x64 3.0.1 and Netbeans 7.3.1. I read the previous issues, but it 
does not work for me. The Runiversal is already installed. The Rscript path is 
correct.
And the problem: "java.lang.RuntimeException: Uncompilable source code - 
Erroneous sym type: rcaller.RCaller.addDoubleArray"
The code: http://paste2.org/7s22wJI3

Thanks,

Original comment by girus.da...@gmail.com on 16 Jul 2013 at 9:15

GoogleCodeExporter commented 8 years ago

ok, I find a the problem :S It's a litle bit frustrating. The problem in the 
code.

Original comment by girus.da...@gmail.com on 17 Jul 2013 at 11:06

GoogleCodeExporter commented 8 years ago

[deleted comment]

GoogleCodeExporter commented 8 years ago

please find the new documentation in site 
http://stdioe.blogspot.com/2013/08/a-user-document-for-rcaller.html

Original comment by mhsatman on 19 Aug 2013 at 6:28

GoogleCodeExporter commented 8 years ago

Hi there
I'm having a very strange behaviour. I tried one of RCaller samples. More 
exactly I tried this simple Java code:

    @Test
    public void test(){
        try {

            /*
             * Creating Java's random number generator
             */
            Random random = new Random();

            /*
             * Creating RCaller
             */
            RCaller caller = new RCaller();
            RCode code = new RCode();
            /*
             * Full path of the Rscript. Rscript is an executable file shipped with R.
             * It is something like C:\\Program File\\R\\bin.... in Windows
             */
            caller.setRscriptExecutable("/usr/bin/Rscript");

            /*
             *  We are creating a random data from a normal distribution
             * with zero mean and unit variance with size of 100
             */
            double[] data = new double[100];

            for (int i = 0; i < data.length; i++) {
                data[i] = random.nextGaussian();
            }

            /*
             * We are transferring the double array to R
             */
            code.addDoubleArray("x", data);

            /*
             * Adding R Code
             */
            code.addRCode("my.mean<-mean(x)");
            code.addRCode("my.var<-var(x)");
            code.addRCode("my.sd<-sd(x)");
            code.addRCode("my.min<-min(x)");
            code.addRCode("my.max<-max(x)");
            code.addRCode("my.standardized<-scale(x)");

            /*
             * Combining all of them in a single list() object
             */
            code.addRCode(
                    "my.all<-list(mean=my.mean, variance=my.var, sd=my.sd, min=my.min, max=my.max, std=my.standardized)");

            /*
             * We want to handle the list 'my.all'
             */
            caller.setRCode(code);
            caller.runAndReturnResult("my.all");

            double[] results;

            /*
             * Retrieving the 'mean' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("mean");
            System.out.println("Mean is " + results[0]);

            /*
             * Retrieving the 'variance' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("variance");
            System.out.println("Variance is " + results[0]);

            /*
             * Retrieving the 'sd' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("sd");
            System.out.println("Standard deviation is " + results[0]);

            /*
             * Retrieving the 'min' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("min");
            System.out.println("Minimum is " + results[0]);

            /*
             * Retrieving the 'max' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("max");
            System.out.println("Maximum is " + results[0]);

            /*
             * Retrieving the 'std' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("std");

            /*
             * Now we are retrieving the standardized form of vector x
             */
            System.out.println("Standardized x is ");

            for (int i = 0; i < results.length; i++) {
                System.out.print(results[i] + ", ");
            }
        } catch (Exception e) {

            e.printStackTrace();
        }
    }
On my machine (ubuntu 12.04) all works pretty good; I tried, then, on my server 
machine (a RedHat machine); I tried the same code; the only difference is that 
since this RedHat machien couldn't access on internet I had to install manually 
R and RUniversal; after I installed them I tried this code (the same of before 
but with differente RScript location):
    @Test
    public void test(){
        try {

            /*
             * Creating Java's random number generator
             */
            Random random = new Random();

            /*
             * Creating RCaller
             */
            RCaller caller = new RCaller();
            RCode code = new RCode();
            /*
             * Full path of the Rscript. Rscript is an executable file shipped with R.
             * It is something like C:\\Program File\\R\\bin.... in Windows
             */
            caller.setRscriptExecutable("/usr/R-2.14.1/bin/Rscript");

            /*
             *  We are creating a random data from a normal distribution
             * with zero mean and unit variance with size of 100
             */
            double[] data = new double[100];

            for (int i = 0; i < data.length; i++) {
                data[i] = random.nextGaussian();
            }

            /*
             * We are transferring the double array to R
             */
            code.addDoubleArray("x", data);

            /*
             * Adding R Code
             */
            code.addRCode("my.mean<-mean(x)");
            code.addRCode("my.var<-var(x)");
            code.addRCode("my.sd<-sd(x)");
            code.addRCode("my.min<-min(x)");
            code.addRCode("my.max<-max(x)");
            code.addRCode("my.standardized<-scale(x)");

            /*
             * Combining all of them in a single list() object
             */
            code.addRCode(
                    "my.all<-list(mean=my.mean, variance=my.var, sd=my.sd, min=my.min, max=my.max, std=my.standardized)");

            /*
             * We want to handle the list 'my.all'
             */
            caller.setRCode(code);
            caller.runAndReturnResult("my.all");

            double[] results;

            /*
             * Retrieving the 'mean' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("mean");
            System.out.println("Mean is " + results[0]);

            /*
             * Retrieving the 'variance' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("variance");
            System.out.println("Variance is " + results[0]);

            /*
             * Retrieving the 'sd' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("sd");
            System.out.println("Standard deviation is " + results[0]);

            /*
             * Retrieving the 'min' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("min");
            System.out.println("Minimum is " + results[0]);

            /*
             * Retrieving the 'max' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("max");
            System.out.println("Maximum is " + results[0]);

            /*
             * Retrieving the 'std' element of list 'my.all'
             */
            results = caller.getParser().getAsDoubleArray("std");

            /*
             * Now we are retrieving the standardized form of vector x
             */
            System.out.println("Standardized x is ");

            for (int i = 0; i < results.length; i++) {
                System.out.print(results[i] + ", ");
            }
        } catch (Exception e) {

            e.printStackTrace();
        }
    }

The result is this error (the full log is attached to the comment):
packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org")
}

x<-c(0.9460408936904934, -0.5551529340765661, -0.35445834679546645, 
-1.51636590395837, 2.2956289121860416, 0.7961003175829097, -0.553206999727886, 
2.315240334505462, -0.017115179285881, 0.6184951794447279, 0.6915152380610504, 
-1.7002491464823233, 0.6264562094568216, -1.1559911633306237, 
0.36967000660952554, 1.963700830941016, 0.9948380757605925, 
-1.1440168002233462, 0.7686385077566624, 0.4260438110910772, 
-1.0140412741048628, -0.36865279696692693, 0.5610950844352786, 
0.28561328328451924, 0.9726717376491374, 0.029346372842546632, 
0.4137343107224211, 0.48776207142308714, 0.9321365198870694, 
-1.6059931811975339, 0.10383129977895356, 0.5000234810742558, 
-0.9307116155449479, 0.23947794756472315, -0.5334831970109568, 
-0.7343565984781026, 0.8307302650200427, -0.8336411751220243, 
0.2303754210890316, 1.0183478980941134, -1.4274204697242634, 
1.9508730713014155, 0.7877908761802193, 0.32647375169584586, 
-1.2600650564760432, 0.24719441363979894, 1.6519367759561165, 
0.19944952688290857, -0.016926808693460468, 2.5535079470367803, 
-1.1329244716942193, 0.1475209963081771, 1.1695222619885026, 
1.6240089994594509, -1.6212519976525093, -0.8559766273780655, 
-1.5891682505694165, 1.522183605412435, -0.5295164167509316, 
0.9842694632961287, 0.934383962317939, 0.6383625582695062, 
-0.005497226459792411, 0.19072525124366085, 0.014204872493350165, 
0.2722833105208218, -1.9043009664640396, 1.5785479645639267, 
0.5038222038212852, 0.8309506251239861, 1.5125093320129204, 
-1.7859379204123993, 0.2975875921160099, -0.479145400721361, 
-0.038933950814963265, 0.6740939785314669, 0.4616697866959242, 
0.07347724181759564, 0.012080002279981822, 1.5181164033923689, 
0.7255854119790351, 0.07480164480677463, 0.19357551184884908, 
0.38118600240068296, -0.6064523197000228, 1.6168512382147002, 
-0.21080943922429346, 0.6489816305321042, 1.0477859123379218, 
-0.5368095480475188, 0.8858732100717299, -1.3513565717588267, 
-0.0017381349589358603, -1.6175074638240021, 1.6136046244199642, 
0.18818103099731928, 3.0417995806180325, 1.0290236224860667, 
-1.0577298998024147, -0.9160535295724807);
my.mean<-mean(x)
my.var<-var(x)
my.sd<-sd(x)
my.min<-min(x)
my.max<-max(x)
my.standardized<-scale(x)
my.all<-list(mean=my.mean, variance=my.var, sd=my.sd, min=my.min, max=my.max, 
std=my.standardized)
cat(makexml(obj=my.all, name="my.all"), file="/tmp/Routput8052211084061009874")

rcaller.exception.ParseException: Can not handle R results due to : 
rcaller.exception.ParseException: Can not parse output: The generated file 
/tmp/Routput8052211084061009874 is empty

And effectively, the XML file was empty. Since I was thinking that it was 
related to my manual installation of R, I tried the this R code in the R shell:
packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org")
}

x<-c(0.9460408936904934, -0.5551529340765661, -0.35445834679546645, 
-1.51636590395837, 2.2956289121860416, 0.7961003175829097, -0.553206999727886, 
2.315240334505462, -0.017115179285881, 0.6184951794447279, 0.6915152380610504, 
-1.7002491464823233, 0.6264562094568216, -1.1559911633306237, 
0.36967000660952554, 1.963700830941016, 0.9948380757605925, 
-1.1440168002233462, 0.7686385077566624, 0.4260438110910772, 
-1.0140412741048628, -0.36865279696692693, 0.5610950844352786, 
0.28561328328451924, 0.9726717376491374, 0.029346372842546632, 
0.4137343107224211, 0.48776207142308714, 0.9321365198870694, 
-1.6059931811975339, 0.10383129977895356, 0.5000234810742558, 
-0.9307116155449479, 0.23947794756472315, -0.5334831970109568, 
-0.7343565984781026, 0.8307302650200427, -0.8336411751220243, 
0.2303754210890316, 1.0183478980941134, -1.4274204697242634, 
1.9508730713014155, 0.7877908761802193, 0.32647375169584586, 
-1.2600650564760432, 0.24719441363979894, 1.6519367759561165, 
0.19944952688290857, -0.016926808693460468, 2.5535079470367803, 
-1.1329244716942193, 0.1475209963081771, 1.1695222619885026, 
1.6240089994594509, -1.6212519976525093, -0.8559766273780655, 
-1.5891682505694165, 1.522183605412435, -0.5295164167509316, 
0.9842694632961287, 0.934383962317939, 0.6383625582695062, 
-0.005497226459792411, 0.19072525124366085, 0.014204872493350165, 
0.2722833105208218, -1.9043009664640396, 1.5785479645639267, 
0.5038222038212852, 0.8309506251239861, 1.5125093320129204, 
-1.7859379204123993, 0.2975875921160099, -0.479145400721361, 
-0.038933950814963265, 0.6740939785314669, 0.4616697866959242, 
0.07347724181759564, 0.012080002279981822, 1.5181164033923689, 
0.7255854119790351, 0.07480164480677463, 0.19357551184884908, 
0.38118600240068296, -0.6064523197000228, 1.6168512382147002, 
-0.21080943922429346, 0.6489816305321042, 1.0477859123379218, 
-0.5368095480475188, 0.8858732100717299, -1.3513565717588267, 
-0.0017381349589358603, -1.6175074638240021, 1.6136046244199642, 
0.18818103099731928, 3.0417995806180325, 1.0290236224860667, 
-1.0577298998024147, -0.9160535295724807);
my.mean<-mean(x)
my.var<-var(x)
my.sd<-sd(x)
my.min<-min(x)
my.max<-max(x)
my.standardized<-scale(x)
my.all<-list(mean=my.mean, variance=my.var, sd=my.sd, min=my.min, max=my.max, 
std=my.standardized)
cat(makexml(obj=my.all, name="my.all"), file="/tmp/Routput8052211084061009874")

By executing it in the R shell, all works pretty good and I can find the file 
Routput8052211084061009874.xml filled and not empty

Do you have any suggestion? How can I solve this issue?

Thank you,
Angelo

Original comment by angelo...@gmail.com on 6 Sep 2013 at 9:33

GoogleCodeExporter commented 8 years ago

Hi there

By debugging on my RedHat machine I saw a strange thing; I just put some prints 
in the class "rcaller.RStreamHandler"; exactly I put this system.out.println 
both on my ubuntu machine and on my redhat machine:
    public void run() {
        if (reader == null) {
            reader = new BufferedReader(new InputStreamReader(stream));
        }
        System.out.println("closeSignal "+closeSignal);
        String s;
        while (!closeSignal) {
            try {
                s = reader.readLine();
                System.out.println("S pari a "+s);
                if (s != null) {
                    for (EventHandler eventHandler : eventHandlers) {
                        eventHandler.messageReceived(name, s);
                    }
                }
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }

Now in my ubuntu machine I got this prints:
closeSignal false
closeSignal false
S pari a Carico il pacchetto richiesto: Runiversal
S pari a null
S pari a null
S pari a null
S pari a null
..
..

On my RedHat machine I got this prints:
closeSignal false
closeSignal false
S pari a Carico il pacchetto richiesto: Runiversal
S pari a Warning message:
S pari a In library(package, lib.loc = lib.loc, character.only = TRUE, 
logical.return = TRUE,  :
S pari a   there is no package called ‘Runiversal’
S pari a Warning: unable to access index for repository  
http://cran.r-project.org/src/contrib
S pari a null
S pari a null
S pari a null

As we can see it seems it's not able in finding the Runiversal package and it 
tryes to go on internet in order to download it but unsuccessfully; the strange 
thing is that in my R console, always on my redhat machine, I have this result:
> packageExist<-require(Runiversal)
> print(packageExist);
[1] TRUE

So what I'm wondering....why from Java it seems that the RUniversal package is 
not installed while from R console it seems to be installed? Do you have any 
suggestion?

Thank you a lot
Angelo

Original comment by angelo...@gmail.com on 6 Sep 2013 at 10:38

GoogleCodeExporter commented 8 years ago

Hi there :) I'm really sorry for the spamming

Now it seems to be working also on the RedHat machine; I don't know exactly why 
but I simply removed and manually installed again the Runiversal package by 
typing this instruction in the R console 
install.packages('/${rUniversalHome}/Runiversal_1.0.2.tar.gz', repos = NULL, 
type="source")

Angelo

Original comment by angelo...@gmail.com on 6 Sep 2013 at 11:12

GoogleCodeExporter commented 8 years ago

Hi.... i have the same issue... it works fine when i use addRCode... but when i 
try to us R_source, or addRCode("source(....)") i get the same error:

rcaller.exception.RCallerParseException: Can not parse the R output: 
org.xml.sax.SAXParseException

I have installed Runiversal, it is loaden when R starts, i have the correct 
path to the Rscript

Original comment by enscant...@gmail.com on 9 Apr 2014 at 4:45

GoogleCodeExporter commented 8 years ago

RCaller 2.2.0 is introduced in page 
http://stdioe.blogspot.com.tr/2014/04/rcaller-220-is-released.html. The new 
version does not depend on the R package Runiversal. 
So the library is more independent, but the logic is same, R XML routines are 
copied in each session. This process seems to be faster compared to R's package 
loading routines.

Original comment by mhsatman on 12 Apr 2014 at 8:28

GoogleCodeExporter commented 8 years ago

I am trying to pass the list from Java to R but I am unable to do that due to 
this issue......Please help me guys 

[Fatal Error] Routput8380818569065806843:1:1: Premature end of file.
packageExist<-require(Runiversal)
if(!packageExist){
install.packages("Runiversal", repos=" http://cran.r-project.org")
}

install.packages("Runiversal")
install.packages("rJava")
plot.new()
v1<-read.csv("D:\eclipse-jee-kepler-SR2-win32-x86_64\hospital-data.xlsx")
cat(makexml(obj=boxplot(v1), name="boxplot(v1)"), 
file="C:/Users/GOURAV~1/AppData/Local/Temp/Routput8380818569065806843")

rcaller.exception.RCallerExecutionException: Can not handle R results due to : 
rcaller.exception.RCallerParseException: Can not parse the R output: 
org.xml.sax.SAXParseException; systemId: 
file:/C:/Users/GOURAV~1/AppData/Local/Temp/Routput8380818569065806843; 
lineNumber: 1; columnNumber: 1; Premature end of file.
    at rcaller.RCaller.runAndReturnResult(RCaller.java:402)
    at com.web.controller.RHandler.rProcess(RHandler.java:41)
    at com.web.controller.ExcelReader.processUploadedFile(ExcelReader.java:127)
    at com.web.controller.ExcelReader.doPost(ExcelReader.java:71)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:755)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
    at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:684)
    at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:501)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
    at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
    at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
    at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1086)
    at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:428)
    at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
    at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1020)
    at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
    at org.eclipse.jetty.server.handler.HandlerList.handle(HandlerList.java:52)
    at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
    at org.eclipse.jetty.server.Server.handle(Server.java:370)
    at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:494)
    at org.eclipse.jetty.server.AbstractHttpConnection.content(AbstractHttpConnection.java:982)
    at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.content(AbstractHttpConnection.java:1043)
    at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:865)
    at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
    at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:667)
    at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
    at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
    at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
    at java.lang.Thread.run(Unknown Source)
Script executed

Original comment by gouravso...@gmail.com on 2 Oct 2014 at 7:04

Attachments:

Rissue.txt

GoogleCodeExporter commented 8 years ago

gouravsonu89 you are using an old version. please try the latest one.

Original comment by mhsatman on 2 Oct 2014 at 8:24

GoogleCodeExporter commented 8 years ago

Hi,

I am using R-3.1.1 in my window 8 can you please send me the latest version
link..

with regards,

Gourav Khare

Original comment by gouravso...@gmail.com on 2 Oct 2014 at 8:52

GoogleCodeExporter commented 8 years ago

gouravsonu89 use the latest version of rcaller.
visit the page http://mhsatman.com/rcaller/

Original comment by mhsatman on 2 Oct 2014 at 11:00

jrmycohen / rcaller

Can not handle R results due to : rcaller.exception.RCallerParseException: Can not parse the R output: org.xml.sax.SAXParseException: Premature end of file #1