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Using Java methods in R

24 messages · Gabor Grothendieck, hill0093, lcn +4 more

Original
hill0093
# 
I just now registered in R forum.
I use Windows because of past history of using windows.
I have been writing and using programs in java for about a decade.
I work with unequal-interval-time-series data files, 1st 5 lines like:
Title Line
CnYrMoDaHrMnScDCMQ,ColSerTit1,ColSerTit2,ColSerTit3,ColSerTit4,
201104212359599999,Ser1Datum1,Ser2Datum1,Ser3Datum1,Ser4Datum1,
201104220059428739,Ser1Datum2,Ser2Datum2,Ser3Datum2,Ser4Datum2,
201104220103369291,Ser1Datum3,Ser2Datum3,Ser3Datum3,Ser4Datum3,
where e.g.Ser4Datum3 is a number, and calendartime unit can be
anywhere from Da down to Q (Quadiseconds), a lot stops at Mn.
Time is same unit throughout any one file.

Getting to the point: I have all of the calendar-linear conversion 
and file reading subroutines as Java methods and would like to 
use them in R. I am not very knowledgeable yet about R.
I need instructions about how to set up and use java in R on Windows.
Can anyone help me with setup instructions then starting with a 
simple Java function (method) call. One problem with Java is that a 
function returns only one item.


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hill0093
# 
No answer to my post, 
so let's try a simpler question. Am I doing this correctly?
I have the RGui with R Console on the screen.
On rhe top pullDowns, Packages > Install Packages > USA(IA)> rJava
Error in .jnew("C:/ad/j/CalqsLin") : 
  java.lang.NoClassDefFoundError: C:/ad/j/CalqsLin

So I got this error which means I don't understand very much.
I go to C:/ad/j and get
C:\ad\j>dir CalqsLin.class
 Volume in drive C has no label.
 Volume Serial Number is 9A35-67A2
 Directory of C:\ad\j
04/23/2011  07:11 AM            14,651 CalqsLin.class
               1 File(s)         14,651 bytes
               0 Dir(s)  104,257,716,224 bytes free

Just to show my intentions, 
I had next wanted to call this java function method:
linTimOfCalqsStgIsLev("201104052359599999",-4) using:
but that will probably also be wrong?
Obviously I don't understand.


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Gabor Grothendieck
#
On Sat, Apr 23, 2011 at 8:32 AM, hill0093 <hill0093 at umn.edu> wrote:
Have a look at the source of other packages that use rJava.  Such
packages are listed at the bottom of this page:
http://cran.r-project.org/web/packages/rJava/index.html

Also note that there is a separate list for R and Java:
http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel
Shekhar
# 
Hi Hill,
I just finished interfacing the C++ with R, i.e. c++ functions from R
and vice versa. Next thing in pipe line is Java and python.
I just wanted to share some of the things which i think might be
useful for you. Reason being whether its a C++, java or any other
compiled language the interface has to be generic in R. That means
mode of interfacing might be different(using different packages Rcpp
for c++, rJava for Java) but the underlying mechanism remains the
same.

For C++ you will be creating a dll ( windows) and .so( *nix) and for
jave you will be using class.
Now for using c++/java functions with in R or vice versa, you first
should check whether the functions are properly loaded in the R symbol
table or not?

If you are unable to call the java functions in R, then probably you
are unable to load the class into the R environment.

A few steps which i have followed in C++ ( i think must be more or
less same conceptually) could be useful for you:

1) I have a c++ file, i compile it using the command R CMD SHLIB
filename.cpp. On successful completion it creates the library. if you
are getting compilation error then you need to check whether the
header files are in proper path or not.

2) Then for using this function is first use to load the library using
the function dyn.load("library path")

3) If the loading is successful i check whether the required function
is properly loaded into the R symbol table or not by using the
function is.loaded("function name")

4) if it returns true, then i call the function by using .C or .Call
function provided by R.
For more information you can see http://groups.google.com/group/brumail/browse_thread/thread/a278dcbb6a8a439a
.

Hope it helps you in someway.

Regards,
Som Shekhar
Mike Marchywka
# 
----------------------------------------
i haven't used rjava yet, I think I installed it on linux
for testing but no real usage, but this message
appears to come from jvm probably because you
specified an aboslute path. You can try this from
command line,




$ ls ../geo/dayte*
../geo/dayte.class

mmarchywka at phlulap01 /cygdrive/c/d/phluant/duphus
$ java ../geo/dayte
Exception in thread "main" java.lang.NoClassDefFoundError: ///geo/dayte
Caused by: java.lang.ClassNotFoundException: ...geo.dayte
??????? at java.net.URLClassLoader$1.run(Unknown Source)
??????? at java.security.AccessController.doPrivileged(Native Method)
??????? at java.net.URLClassLoader.findClass(Unknown Source)
??????? at java.lang.ClassLoader.loadClass(Unknown Source)
??????? at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
??????? at java.lang.ClassLoader.loadClass(Unknown Source)
Could not find the main class: ../geo/dayte.? Program will exit.


you want to search for the classpath and set that up then
refernce the class name not the path ( the class loader will follow
the path looking for it ). 
Not sure how you do that in rjava under 'dohs but
if you search for that term is should be apparent.
And of course 'dohs and pdf aren't always friendly
for automated work so get something like cygwin and
reduce pdf's to text etc.
Mike Marchywka
# 
----------------------------------------
It appears that by default the current directory is on the
classpath. I must have installed this on 'dohs before
and if I copy the class file into R directory it
can find it,
Error in .jnew("foo") : java.lang.NoClassDefFoundError: foo
[1] "Java-Object{dayte at 1de3f2d}"
that's unlikely to fix all your problems, you want to set the classpath
but if you know the term and can load cygwin you should be able
to find the way to set that up.
hill0093
# 
Hi Shekhar, Thank you. Right path.
Sounds good. Please help me when you discover Java interface.
Firstly, I don't know what the R symbol table is or how to do 
the checking you suggest. I am really naive about R.
I want to be able to get my data in there so I  can learn to use 
it for my purposes.
Hill

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hill0093
# 
Thanks Icn, for suggesting .jaddClassPath
I finally had time to play around and discover what you meant.
So I am one step farther than the report in the second post above:
I have the RGui with R Console on the screen.
On the top pullDowns, Packages > Install Packages > USA(IA)> rJava
[1] "C:\\Users\\ENVY17\\Documents\\R\\win-library\\2.12\\rJava\\java"
[2] "C:\\ad\\j"
Error in .jcall(qsLin, returnSig = "D", "linTimOfCalqsStgIsLev",
"201104052359599999",  : 
  method linTimOfCalqsStgIsLev with signature
(Ljava/lang/String;Ljava/lang/String;)D not found
What's wrong?
Just to show my intentions, 
I had next wanted to call this java function method:
linTimOfCalqsStgIsLev("201104052359599999",-4) 


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hill0093
# 
So I am one step farther than last time, so I am happy:
I have the RGui with R Console on the screen.
On the top pullDowns, Packages > Install Packages > USA(IA)> rJava
[1] "C:\\Users\\ENVY17\\Documents\\R\\win-library\\2.12\\rJava\\java"
[2] "C:\\ad\\j"
[1] "201104242359599999"
[1] 634709087999999
[1] "201104242359599999"
[1] 634709087999999
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hill0093
# 
I added this R code to the bottom of the previous code and it doesn't work
[[1]]
[1] "Java-Array-Object[D:[D at 8813f2"

[[2]]
[1] "Java-Array-Object[D:[D at 1d58aae"

[[3]]
[1] "Java-Array-Object[D:[D at 83cc67"
Error in print(ar34Ret(i, j), digits = 15) : 
  could not find function "ar34Ret"
The Java code is:
public final static double[][] arReturnTEST() { 
  double[][]retArr=new double[3][4]; for(int i=0;i<3;i++)for(int
j=0;j<4;j++)retArr[i][j]=i*1000+j; return(retArr); 
} 
R doesn't know how to print the array in the next to final line,
and thinks the array is a function in the final line.

Any suggestions?


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hill0093
# 
So the first few posts show that I found out how to 
get Java functions to return type double numbers to R.
The arrays are still a problem.

Here is another of my attempts to understand how to get java arrays into R.
The Java code in class CalqsLin for an array 
of constants named conArr and for a function returning an array is:
public static double[][]conArr=new double[][] { { 10001,10002,10003,10004
},{ 20001,20002,20003,20004 },{ 30001,30002,30003,30004 } }; 
public final static double[][] arReturnTEST() { 
  double[][]retArr=new double[3][4]; for(int i=0;i<3;i++)for(int
j=0;j<4;j++)retArr[i][j]=i*1000+j; return(retArr); 
} 

I evidently do not know how to retrieve them in R, even with .jevalArray():
Error in .jevalArray(arj34Ret) : 
  object is not a Java object reference (jobjRef/jarrayRef).
Error in .jevalArray(qsLin.conArr) : object 'qsLin.conArr' not found

I need help from someone who calls Java from R.
The whole session was:
[1] "C:\\Users\\ENVY17\\Documents\\R\\win-library\\2.12\\rJava\\java"
[2] "C:\\ad\\j"
[1] "201104242359599999"
[1] 634709087999999
[1] "201104242359599999"
[1] 634709087999999
Error in .jevalArray(arj34Ret) : 
  object is not a Java object reference (jobjRef/jarrayRef).
Error in .jevalArray(qsLin.conArr) : object 'qsLin.conArr' not found
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hill0093
# 
Thanks Icn for pointing that out, but I don't understand it.
My use of .jcall to return a type double scalar or String worked.
My use of .jfield to get a one dimensional static array worked.
My use of .jfield to get a static scalar constant did not work.
My use of .jfield to get a two dimensional static constant array did not
work.
I don't understand the remainder of my rjava trial.

The C:/ad/j/CalqsLin java code is:
  public final static double con0dbl=10001; 
  public final static double[]con1Arr=new double[] {
10001,10002,10003,10004,10005,10006 }; 
  public final static double[][]con2Arr=new double[][] { {
10001,10002,10003,10004 },{ 20001,20002,20003,20004 },{
30001,30002,30003,30004 } }; 
  public final static double[][] arReturnTEST() { 
    double[][]retArr=new double[3][4]; for(int i=0;i<3;i++)for(int
j=0;j<4;j++)retArr[i][j]=i*1000+j; return(retArr); 
  } 
I have the RGui with R Console on the screen; here is the trial:
On the top pullDowns: Packages > Install Packages > USA(IA)> rJava
[1] 0
[1] "C:\\Users\\ENVY17\\Documents\\R\\win-library\\2.12\\rJava\\java"
[2] "C:\\ad\\j"
[1] "201104242359599999"
[1] 634709087999999
[1] "201104242359599999"
[1] 10001 10002 10003 10004 10005 10006
Error in .jfield(qsLin, sig = "D", "con0dbl") : 
  RgetField: field con0dbl not found
[[1]]
NULL
[[1]]
[1] "Java-Array-Object[D:[D at 1d58aae"
[[2]]
[1] "Java-Array-Object[D:[D at 83cc67"
[[3]]
[1] "Java-Array-Object[D:[D at e09713"
Error in .jevalArray(arj34Ret) : 
  object is not a Java object reference (jobjRef/jarrayRef).
Error in print(ar34Ret[2][3], digits = 15) : object 'ar34Ret' not found
Error in print(ar34Ret, digits = 20) : object 'ar34Ret' not found
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hill0093
# 
Thanks Icn for the lookup.
I appreciate your skill.
The static double field con0dbl started working for me too.
I was surprised, and checked my code carefully.
I think they corrected that in rJava.
I download and install rJava each time I use R.
Hill


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hill0093
# 
I don't know who to contact in the management of this R-forum,
and there are a few things I cannot figure out.

As I understand it, to participate and learn on the R-forum,
I must receive all the emails even concerning topics I have no
interest in currently. It clogs up my email, takes a long 
time to delete, and is hard to be selective enough to not
delete some of my other important email. It is nice to 
receive email on my posts and possibly even those others that
I have responded to. Do I understand this correctly?

Another item is that rJava has existed and has been promoted for 
a long time, and yet it doesn't seem to work for even some 
simple things like getting exactly-rectangular arrays from 
Java classes. Of course it could be that I just don't know 
how to use it, but people on the forum don't seem to know 
either. Maybe the people that know don't use the forum because
of all the email.

Or maybe there are not enough people that are writing rJava. 
And I am not talented enough to do so.



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1 day later
hill0093
# 
H do I obtain a strictly rectangular
type-double array (converted to an R 2-dimensional array) from a Java class? 
I can obtain a 1-dimensional type-double array (vector) or a scalar, 
but I cannot figure out the two-dimensional from the instructions.
Is .jevalArray also involved?
My simple Java test class and R test code follows:

import java.lang.reflect.Array;
public class RJavTest { 
  public static void main(String[]args) { RJavTest rJavTest=new RJavTest();
} 
  public final static String conStg="testString"; 
  public final static double con0dbl=10001; 
  public final static double[]con1Arr=new double[] {
10001,10002,10003,10004,10005,10006 }; 
  public final static double[][]con2Arr=new double[][] { {
10001,10002,10003,10004 },{ 20001,20002,20003,20004 },{
30001,30002,30003,30004 } }; 
  public final static String retConStg() { return(conStg); } 
  public final static double retCon0dbl() { return(con0dbl); } 
  public final static double[] retCon1Arr() { return(con1Arr); } 
  public final static double[][] retCon2Arr() { return(con2Arr); } 
}

library(rJava)
.jinit()
.jaddClassPath("C:/ad/j")
print(.jclassPath())
rJavaTst <- .jnew("RJavTest")
conn1Arr <- .jfield(rJavaTst,sig="[D","con1Arr")
print(conn1Arr)
print(conn1Arr[2])
conn1ArrRet <- .jcall(rJavaTst,returnSig="[D","retCon1Arr")
print(conn1ArrRet)
print(conn1ArrRet[2])
conn0dbl <- .jfield(rJavaTst,sig="D","con0dbl")
print(conn0dbl)
##The above works, but not the following
conn2Arr <- .jfield(rJavaTst,sig="[[D","con2Arr")
print(conn2Arr[2])
print(conn2Arr[2,3])
print(conn2Arr)
arj34Ret <- .jcall(rJavaTst,returnSig="[[D","arReturnTEST")
print(arj34Ret)

The latter 2-dim stuff doesn't work



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Robert Baer
# 
-- snip --
-- snip --

If you don't care about contributing to the R listserve community, it's hard 
to imagine why that community should care about you.

Some people (not me) seem to use nabble [ http://www.nabble.com/ ] to 
monitor the list.  See "R" under "what is cool" .  Another option is to set 
up "rules" in your email client to direct your mail to an appropriate 
folders or if you use gmail I guess we would say to "label" you R listserve 
email.

You can search mail archives for a topic of interest with the R command line 
command
RSiteSearch().  To learn more type
?RSiteSearch

For fun I put rJava rectangular arrays into this search engine (having no 
idea what  that means) and one of the things that came out was:
http://finzi.psych.upenn.edu/R/library/rJava/html/jrectRef-class.html

Hopefully, this or one of the other things can be useful to you.

Finally for the third time, try joining/looking at:
stats-rosuda-devel:
   http://mailman.rz.uni-augsburg.de/mailman/listinfo/stats-rosuda-devel
or the archive:
  http://mailman.rz.uni-augsburg.de/pipermail/stats-rosuda-devel/

------------------------------------------
Robert W. Baer, Ph.D.
Professor of Physiology
Kirksville College of Osteopathic Medicine
A. T. Still University of Health Sciences
800 W. Jefferson St.
Kirksville, MO 63501
660-626-2322
FAX 660-626-2965