gmane.comp.lang.r.rosuda.devel

Possible bug in REXPDouble.NA?

Víctor Pascual Cid — 2012-05-06T15:09:42

Hi there,

The value of REXPDouble.NA seems to be NaN, while in REXPInteger and REXPLogical has a specific value. Is that correct, or it can be considered as a bug?

System.out.println("Double NA: " + REXPDouble.NA);
System.out.println("Integer NA: " + REXPInteger.NA);
System.out.println("Logical NA: " + REXPLogical.NA);

Double NA: NaN
Integer NA: -2147483648
Logical NA: -128

Cheers,

Víctor

Unable to run Rserve -dbg version

Suresh Krishna — 2012-04-24T15:44:35

Hello,

I am having some trouble trying to run Rserve-dbg.so on Mac OS 10.6.

I am using:

alias Rservedbg="R CMD  
/Library/Frameworks/R.framework/Versions/Current/Resources/library/Rserve/libs/x86_64/Rserve-dbg.so"

Now:

Suresh-iMac:~ suresh$ Rservedbg
WARNING: ignoring environment value of R_HOME
Rserve 0.6-8 (338) (C)Copyright 2002-2011 Simon Urbanek
$Id: Rserv.c 338 2012-02-11 20:52:25Z urbanek $

Loading config file /etc/Rserv.conf
Failed to find config file /etc/Rserv.conf

R version 2.15.0 (2012-03-30)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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.

   Natural language support but running in an English locale

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

iplots : Moving points

Mohit Dayal — 2012-03-31T11:19:09

Dear Rosuda group,

I am trying to develop an interactive clustering tool for which I require a
graphics system that allows one to move points interactively. (That is, the
user can brush one or more points, and then when the mouse is dragged, the
points move along). GGobi has a nice implementation of this, but that
system does not really provide me with all that I need (especially
close Rintegration). Therefore I would like to work with
iplots and add this feature.

I've gone through the source of iplots (at least the R side of things) and
I see the function ivar.update. This would do quite nicely for me, but I've
not been able to work out how to make iplots recognize a mouse drag event.
(I'm guessing this needs the java side?) I would appreciate any and all
help in this regard, and am ready to code the required parts myself.

Best,
Mohit Dayal
Researcher
Applied Statistics and Computing Lab
Indian School of Business
Hyderabad, India
www.isb.edu

Rserve server problems

Michael Bach — 2012-03-28T11:42:35

Hi!

We are trying to use Rserve at work. I am using Rserve 0.6.1 on a Debian
VirtualBox virtual machine as guest and a Windows 7 as host. I want to
access Rserve through a little Java program as a test whether the port
forwarding from localhost port 6311 to debian guest OS works (so Rserve can
be accessed from the network). I checked whether the server is accepting
connections via `telnet localhost 6311' from the debian guest - and it
does. I then tried to connect from the Windows OS via this small Java
program:

import org.rosuda.REngine.*;
import org.rosuda.REngine.Rserve.*;

public class Rserve_test {
    public static void main(String[] args) {
        try {
            System.out.println("test");
            RConnection c = new RConnection("localhost", 6311);
            REXP x = c.eval("R.version.string");
            System.out.println(x.asString());
        } catch (Exception ex) {
        ex.printStackTrace();
        }
    }
}

This fails with the backtrace:

org.rosuda.REngine.Rserve.RserveExcept

How to use Rengine

I.Andoh — 2012-03-23T14:20:11

Dear sir;
Although the re operate with the following sample programs
the re2 does not operate but it becomes fatal error.
Please let me know whether what I should do.


import org.rosuda.JRI.REXP;
import org.rosuda.JRI.Rengine;
public class Rsample
{
    public static void main(String[] args)
    {

          Rengine re = new Rengine (new String[]{"--no-save"}, false, null);
        re.assign("a", new int[]{36});
        REXP result = re.eval("sqrt(a)");
        System.out.println(result.asDouble());
        re.end();

                  Rengine re2 = new Rengine (new String[]{"--no-save"}, 
false, null);
        re2.assign("b", new int[]{36});
        REXP result2 = re2.eval("sqrt(b)");
        System.out.println(result2.asDouble());
        re2.end();

}
}

error message
run:
6.0
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  Internal Error (0xc0000029), pid=6332, tid=11692
#
# JRE version: 7.0_02-b13
# Java VM: Java HotSpot(TM) Client VM (22.0-b10 mixed mode, sharing 
windows-x86

Why JGR looks so different?

Iurie Malai — 2012-03-20T15:00:56

When I start JGR as a normal user, it looks like here:
http://farm7.staticflickr.com/6233/7000076003_8384b0662c_m.jpg.
When I start JGR with 'sudo' (as root), it looks like here:
http://farm8.staticflickr.com/7069/6853951548_c8964a08d5_m.jpg.
Why? From my point of view the second option is more clear (and
pleasant), but this is not a reason to run JGR everytime as a root.
Can I change this?

Regards,
Iurie Malai

How to install GNU R, JGR and Deducer in Ubuntu
https://sites.google.com/site/iuriemalai/en/how-to-install-gnu-r-jgr-and-deducer-in-ubuntu

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Rengine kill

I.Andoh — 2012-03-18T23:11:24

Hello

I don’t kill Rengine.
I run next proguram but can’t  execute  “re.end();”.

How to kill the progran.

package jrtest;

import org.rosuda.JRI.REXP;
import org.rosuda.JRI.Rengine;

public class  JRtest {
public static void main(String[] args) {
      if (!Rengine.versionCheck()) {
        System.err.println("** Version mismatch - Java files don't match 
library version.");
        System.exit(1);
    }
    //start
     Rengine re = new Rengine (new String[]{"--no-save"}, false, null);

   double fluct[]={
         -1.510061151, -1.483533210 ,-2.454857885 
,-1.582381336, -2.189866550
, -1.259217396 , 0.122006351 ,-0.680441673 , 0.148050467 ,-0.424794143
, -0.606838795, -0.799486016 ,-0.184970425 , 0.666686479 ,-0.377533334
, -1.320383326, -0.756885509, -0.438778336 ,-1.031146806 , 0.191056368
, -1.154535333 ,-0.132690188 , 0.513218124  ,0.988845215 , 1.649814052
,  0.927037224 , 0.627193855 , 1.149564715 , 0.284609312 ,-0.054383389
, -0.645675322, -0.512513869 ,-0.443688139 , 0.148951284, -0.4801

How to kill/close JGR window from R concole?

Iurie Malai — 2012-03-07T18:38:15

Is this possible to kill JGR Console from R (in terminal)?
(I know how to close JGR from his own menu).

Regards,
Iurie

Setting JGR as default R editor on Windows

Muenchen, Robert A (Bob — 2012-02-28T13:40:27

Hi All,

I'd like to set JGR's program editor to be my default for R programs on my Windows 7 system. I tried right-clicking on an R script and changing its "open with" property to JGR.exe. Now when I double-click on a file with a ".R" extension, JGR starts, but it does not open the file into its program editor. If I follow the exact same steps to return to RSTudio, it works just fine. Is there a setting I'm missing?

Thanks,
Bob

=========================================================
  Bob Muenchen (pronounced Min'-chen), Manager  
  Research Computing Support
  Voice: (865) 974-5230  
  Email: muenchen< at >utk.edu
  Web:   http://oit.utk.edu/research, 
  News:  http://oit.utk.edu/research/news.php
========================================================

Kafka consumer java client in R

Harsh — 2012-02-27T13:26:39

I am looking to bring the Kafka consumer in R.
Kafka is a messaging system and produces-consumes events which are
encoded as Binary Avro format. In trying to consume these messages in
real time, many clients are available but none in R.

A pure R solution may not be viable, and I wanted to try my hands at
integrating the Java consumer client in R since the rJava package
makes it possible.

In doing so, I have to admit my limited Java programming skills and
not a very in-depth understanding of R internals and seek
advice/suggestions from expert users and developers on this list.

A few links to add more context to this goal;

Apache Kafka : http://incubator.apache.org/kafka/
Kafka Clients : https://github.com/apache/kafka/tree/trunk/clients
Related SO question :
http://stackoverflow.com/questions/9432045/kafka-consumer-in-r

I have looked at the tutorial
http://cran.r-project.org/web/packages/helloJavaWorld/vignettes/helloJavaWorld.pdf
and could understand at a very high-level what rJava facilitates.

Any sug

Regarding problem of connecting to Rserve

2012-02-26T21:07:21

Dear Simon,
We are using Rserve to perform computations for enrichment analysis in  
R and using bioconductor. Our server is linux. We are trying to  
dispaly the results on the web after performing necessary actions on  
the server which is linux. While performing the computations first  
time we are getting the result, but at the next instance we get an  
error (Null point exception error).

When we do this

FIX:
===
stopping the processes

sudo kill 7335
sudo kill -9 19371

and restarting RServe

it works and again it breaks

we think

non-functional instance of Rserve was already running (?)

7335 ?        Ss
0:04 /usr/local/lib/R/site-library/
Rserve/libs//Rserve-bin.so
19371 ?
S      0:00 /usr/local/lib/R/site-library/Rserve/libs//Rserve-bin.so
19500 pts/5    S+     0:00 grep Rserve

It would be of great help if you can please let us a solution for this  
problem. We are new in using Rserve. We like to know from where the  
possible error is occuring. Thanks for you help in advance

Regards,
Ravi


Her

Warnings when installing JGR

Iurie Malai — 2012-02-26T10:18:10

I have installed JGR in Ubuntu 10.04.4 and it works, but I received a list
of 14 warnings:

There were 14 warnings (use warnings() to see them)

This is the clean list of packages with non-zero exit status:
latentnet, rgdal, rgeos, rgl, Rmpi, RODBC, rpvm, rsprng, shapes, statnet,
tikzDevice, tkrplot, VIM, XML

I reinstalled (without uninstalling) repeatedly JGR with the command
'install.packages('JGR', dep=TRUE)', no packages were installed but one
(JGR_1.7-9.tar.gz) and these warnings do not apeared again. Is this normal?

rserve - java heap space issue when runningcorrelation function

Anish Kejariwal — 2012-02-17T23:47:45

Hello,

I'm trying to run the R's correlation (cor) function via rserve.

Here's my java code:
RList l = new RList();
for (String id : namedVectorList.keySet()) {
  Double[] values = namedVectorList.get(id);
  double[] valuePrimitiveArray = ArrayUtils.toPrimitive((Double[]) values);
   l.put(id, new REXPDouble(valuePrimitiveArray));
}
rConn.assign("corDataFrame", REXP.createDataFrame(l));
corrMatrix = rConn.eval("cor(corDataFrame)").asDoubleMatrix();

When I run this on small amounts of data, it works fine.   But, on this
larger amount of data  (15,000 objects added to RList, and each has 200
Double values in each of the Double arrays), I run into the following issue:

Caused by: java.lang.OutOfMemoryError: Java heap space
at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:218)
at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:180)
at org.rosuda.REngine.Rserve.protocol.RTalk.request(RTalk.java:250)
at org.rosuda.REngine.Rserve.RConnection.eval(RConnection.java:231)

In the Rserve.con

Problems generating a data frame from a tablewith blank cells

Víctor Pascual Cid — 2012-02-13T17:01:14

Hi all,

I've built my own system that uses Rserve to map my Java objects into R variables. Nevertheless, I'm having issues when dealing with tables that contain blank cells.
Here is an example:

"","",""
"aaa","bbb","ccc"
1,2,3
1,2,3

The content of the previous table (encoded as csv) is actually a java ArrayList filled with ArrayLists that gets converted into a RList filled with three RLists, each one containing two REXPStrings and two REXPIntegers.
When trying to run the following code Rserve fails with a "java.lang.ArrayIndexOutOfBoundsException: 0" (it does not even throw a RServerException).

REXP rexp = REXP.createDataFrame(rList);
myRConnection.assign(rexp),

Nevertheless, if I internally replace blank cells with "_", everything seems to work.

How can I create data frames with blank cells?

Cheers,

Víctor

How to start JGR as a full sized window?

Iurie Malai — 2012-02-09T05:29:51

I want to start JGR as a full sized/maximized window automatically, but how
to do this? For other applications I can add option "--geometry 1440x900"
to the launch command, but for JGR this do not work. Sugestions?

Unable to recover column names from a matrix

Víctor Pascual Cid — 2012-02-08T16:19:04

I think I've found a bug related to the recovery of column names in matrices.

The following R command generates a matrix with two name columns: b<- as.matrix(data.frame(a=c(1, 2), b=c(1,2)))
Nevertheless, instead of returning a Map with the names and values, RConnection.eval returns a REXPDouble that makes impossible to get the names of the columns.

Hope that helps to improve the package,

Víctor

Questions about JGR's program editor

Muenchen, Robert A (Bob — 2012-02-06T16:08:01

Hi All,

I'm having several problems with JGR on Windows 7. First, when I open a file that is several layers down in the directory structure, then I need to open another file that's in a higher level, the folder with the green upward-pointing arrow at the top of the Open dialog will not move the Open dialog upward through the directory structure. However, if I use the "Look in:" box to move one level upward in the directory structure, then the green upward-pointing arrow will start to work and I can move as many layers up as I like. Each time the Open dialog is used, it reverts to blocking upward movement. Is this a bug or can I change a setting somewhere to get it to go upward?

Second, the mouse selection speed is way too fast toward the top or bottom of the program editor. If I'm near the center of the editor window, it's easy to select a few lines of code. But if I'm at the top or bottom of the window, as soon as I pass the 2nd or 3rd line, the selection blasts into high gear and I end up having selected

Executing Control commands in Rserve from theR client

Daniel Chapsky — 2012-01-27T15:19:24

Hi all ,


Does anybody have any insight to how control commands might
be implemented from the R client for Rserve? So far I've
tried implementing CMD_ctrlEval command from the QAP1 protocol by altering
the current RSeval code thusly:

RSevalControl <- function(c, expr) {
r <- if (is.character(expr))
serialize(parse(text=paste("{",paste(expr,collapse="\n"),"}"))[[1]],NULL)
else serialize(expr, NULL)
writeBin(c(0x42L, length(r), 0L, 0L), c, endian="little")
writeBin(r, c)

##b <- readBin(c,"int",4,endian="little") # the return lines commented out
because I dont' think the control commands are supposed to return anything
}

Anybody have any pointers on how I could get this working?

Thanks

iplots bug question

John Thompson — 2012-01-26T22:19:21

Hello,

I'm running R version 2.14.1 on a 64bit Windows 7 machine.  When I try to
run iplots I get this error message:

Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: fun(libname, pkgname)
  error: JAVA_HOME cannot be determined from the RegistryError:
package ‘rJava’ could not be loaded


I have installed rJava however, there appears to be an error with
rJava similar to that observed in Unix systems.


Do you have any suggestions for a solution.


Thank you,

 John Thompson

R Code With Try Catch Block

Dario Strbenac — 2012-01-24T02:00:10

Hello,

I have a small example of when using JRI and there is an error in a try catch block, it is not caught within R, but causes problems in Java. I get output of a number of non alphabetic characters.

When I run the same code in standalone R, I get it working fine.

Loading required package: Rsamtools
Loading required package: IRanges

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:base’:

    cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: RCurl
Loading required package: bitops
[1] "http://genomesavant.com/savant/data/hg19/hg19.refGene.gz"

Whereas, when I'm running the Java program and using JRI to do the same, below is a screenshot of what happens. Stepping through the java code, it's definitely the line rExec.parseAndEval("tmp <- updateURL(x)"); where it happens.

A few more bugs in REXP.asNativeJavaObject

Víctor Pascual Cid — 2012-01-19T17:31:17

Hi there,

playing around with the  method REXP.asNativeJavaObject I've found a few things that look like possible bugs:

- "data.frame(1:20) * 4"  returns a HashMap whose key is the array itself (numbers from 4 to 80) and value is the name of the value. I guess that this is the other way around: they key should be 1.20 and the value the array with the values

- While creating a data frame using REXP.createDataFrame works well, multiplying such data frame by a number returns a REXPGenrericVector with an empty Object[] inside.

That's the code that I'm using to build the data frame
RList rList = new RList();
for (int i = 0; i<numColumns; i++) {
column = (int[])getColumn();
rList.add(REXPWrapper.wrap(column));
}

Hope that feedback is helpful.

Víctor