I have build an application connecting R and java using the RServe package. In this project I use neuralnet to predict output. Where is the source code that I use are as follows:
myneuralnetscript=function(){
trainingData = read.csv("D:\\Kuliah\\Semester V\\TA\\Implementasi\\training.csv")
testingData = read.csv("D:\\Kuliah\\Semester V\\TA\\Implementasi\\testing.csv")
X1training <- trainingData$open
X2training <- trainingData$high
X3training <- trainingData$low
X4training <- trainingData$close
X5training <- trainingData$volume
targetTraining <- trainingData$target
X1testing <- testingData$open
X2testing <- testingData$high
X3testing <- testingData$low
X4testing <- testingData$close
X5testing <- testingData$volume
targetTesting <- testingData$target
xTraining <- cbind(X1training,X2training,X3training,X4training,X5training)
sum.trainingData <- data.frame(xTraining,targetTraining)
net.sum <- neuralnet(targetTraining~X1training+X2training+X3training+X4training+X5training, sum.trainingData, hidden=5,act.fct="logistic")
xTesting <- cbind(X1testing,X2testing,X3testing,X4testing,X5testing)
sum.testingData <- data.frame(xTesting,targetTesting)
result <- compute(net.sum,sum.testingData[,1:5])
return(result)
}
The output generated as follows:
Here the program from Java to access the results of the R.
public static void main(String[] args) {
RConnection connection = null;
try {
/* Create a connection to Rserve instance running on default port
* 6311
*/
connection = new RConnection();
//Directory of R script
connection.eval("source('D:\\\\Kuliah\\\\Semester V\\\\TA\\\\Implementasi\\\\R\\\\neuralNet.R')");
//Call method
double output = connection.eval("myneuralnetscript()").asDouble();
System.out.println(output);
} catch (RserveException | REXPMismatchException e) {
System.out.println("There is some problem indeed...");
}
}
However, the output that appears is "There is some problem indeed ...".
Please do not catch exceptions just to print a useless message. Remove your try catch and declare main to throw Exception. That way you'll see the actual error.
Either Rserve is not running locally on 6311 or it's failing to evaluate or the result of second evaluation cannot be coerced into a single double.
When you run eval do
tryCatch({CODE},e=function ()e)
instead and check if return inherits from try-error and get the message
Related
I am trying to access a java program MELTING 5 in R using the rjava package.
I can do it using the system function as follows using the batch file.
path <- "path/to/melting.bat"
sequence = "GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTTCCAC"
hybridisation.type = "dnadna"
OligomerConc = 5e-8
Sodium = 0.05
command=paste("-S", sequence,
"-H", hybridisation.type,
"-P", OligomerConc,
"-E", paste("Na=", Sodium, sep = ""))
system(paste("melting.bat", command))
I am trying to do the same using a wrapper, following the steps in hellowjavaworld without any success.
.jaddClassPath('path/to/melting5.jar')
main <- .jnew("melting/Main")
out <- .jcall(obj = main, returnSig = "V", method = "main", .jarray(list(), "java/lang/String"),
argument = command)
The java code in melting/Main.java in the melting5.jar that I am trying to access is as follows.
package melting;
import java.text.NumberFormat;
import melting.configuration.OptionManagement;
import melting.configuration.RegisterMethods;
import melting.methodInterfaces.MeltingComputationMethod;
import melting.nearestNeighborModel.NearestNeighborMode;
/**
* The Melting main class which contains the public static void main(String[] args) method.
*/
public class Main {
// private static methods
/**
* Compute the entropy, enthalpy and the melting temperature and display the results.
* #param args : contains the options entered by the user.
* #param OptionManagement optionManager : the OptionManegement which allows to manage
* the different options entered by the user.
*/
private static ThermoResult runMelting(String [] args, OptionManagement optionManager){
try {
ThermoResult results =
getMeltingResults(args, optionManager);
displaysMeltingResults(results);
return results;
} catch (Exception e) {
OptionManagement.logError(e.getMessage());
return null;
}
}
/**
* Compute the entropy, enthalpy and melting temperature, and return
* these results.
* #param args options (entered by the user) that determine the
* sequence, hybridization type and other features of the
* environment.
* #param optionManager the {#link
* melting.configuration.OptionManagement
* <code>OptionManagement</code>} which
* allows the program to manage the different
* options entered by the user.
* #return The results of the Melting computation.
*/
public static ThermoResult getMeltingResults(String[] args,
OptionManagement optionManager)
{
NumberFormat format = NumberFormat.getInstance();
format.setMaximumFractionDigits(2);
// Set up the environment from the supplied arguments and get the
// results.
Environment environment = optionManager.createEnvironment(args);
RegisterMethods register = new RegisterMethods();
MeltingComputationMethod calculMethod =
register.getMeltingComputationMethod(environment.getOptions());
ThermoResult results = calculMethod.computesThermodynamics();
results.setCalculMethod(calculMethod);
environment.setResult(results);
// Apply corrections to the results.
results = calculMethod.getRegister().
computeOtherMeltingCorrections(environment);
environment.setResult(results);
return environment.getResult();
}
/**
* displays the results of Melting : the computed enthalpy and entropy (in cal/mol and J/mol), and the computed
* melting temperature (in degrees).
* #param results : the ThermoResult containing the computed enthalpy, entropy and
* melting temperature
* #param MeltingComputationMethod calculMethod : the melting computation method (Approximative or nearest neighbor computation)
*/
private static void displaysMeltingResults(ThermoResult results)
{
NumberFormat format = NumberFormat.getInstance();
format.setMaximumFractionDigits(2);
MeltingComputationMethod calculMethod =
results.getCalculMethod();
double enthalpy = results.getEnthalpy();
double entropy = results.getEntropy();
OptionManagement.logInfo("\n The MELTING results are : ");
if (calculMethod instanceof NearestNeighborMode){
OptionManagement.logInfo("Enthalpy : " + format.format(enthalpy) + " cal/mol ( " + format.format(results.getEnergyValueInJ(enthalpy)) + " J /mol)");
OptionManagement.logInfo("Entropy : " + format.format(entropy) + " cal/mol-K ( " + format.format(results.getEnergyValueInJ(entropy)) + " J /mol-K)");
}
OptionManagement.logInfo("Melting temperature : " + format.format(results.getTm()) + " degrees C.\n");
}
// public static main method
/**
* #param args : contains the options entered by the user.
*/
public static void main(String[] args) {
OptionManagement optionManager = new OptionManagement();
if (args.length == 0){
optionManager.initialiseLogger();
optionManager.readMeltingHelp();
}
else if (optionManager.isMeltingInformationOption(args)){
try {
optionManager.readOptions(args);
} catch (Exception e) {
OptionManagement.logError(e.getMessage());
}
}
else {
runMelting(args, optionManager);
}
}
}
How to pass arguments in command to public static void main in java jar?
Over at https://github.com/hrbrmstr/melting5jars I made a pkg wrapper for the MELTING 5 jar (melting5.jar) and also put the Data/ directory in it so you don't have to deal with jar-file management. It can be installed via devtools::install_github("hrbrmstr/melting5jars"),
BEFORE you load that library, you need to set the NN_PATH since the Data/ dir is not where the jar expects it to be by default and you may run into issues setting it afterwards (YMMV).
NOTE: I don't work with this Java library and am not in your field, so please double check the results with the command-line you're used to running!
So, the first things to do to try to get this to work are:
Sys.setenv("NN_PATH"=system.file("extdata", "Data", package="melting5jars"))
library(melting5jars) # devtools::install_github("hrbrmstr/melting5jars")
Now, one of the cooler parts of rJava is that you get to work in R (code) if you want to vs Java (code). We can recreate the core parts of that Main class right in R.
First, get a new melting.Main object and a new OptionManagement object just like the Java code does:
melting <- new(J("melting.Main"))
optionManager <- new(J("melting.configuration.OptionManagement"))
Next, we setup your options. I left Sodium the way it is just to ensure I didn't mess anything up.
Sodium <- 0.05
opts <- c(
"-S", "GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTTCCAC",
"-H", "dnadna",
"-P", 5e-8,
"-E", paste("Na=", Sodium, sep = "")
)
Now, we can call getMeltingResults() from that Main class directly:
results <- melting$getMeltingResults(opts, optionManager)
and then perform the same calls on those results:
calculMethod <- results$getCalculMethod()
enthalpy <- results$getEnthalpy()
entropy <- results$getEntropy()
if (.jinstanceof(calculMethod, J("melting.nearestNeighborModel.NearestNeighborMode"))) {
enthalpy <- results$getEnergyValueInJ(enthalpy)
entropy <- results$getEnergyValueInJ(entropy)
}
melting_temperature <- results$getTm()
enthalpy
## [1] -1705440
entropy
## [1] -4566.232
melting_temperature
## [1] 72.04301
We can wrap all that up into a function that will make it easier to call in the future:
get_melting_results <- function(opts = c()) {
stopifnot(length(opts) > 2) # a sanity check that could be improved
Sys.setenv("NN_PATH"=system.file("extdata", "Data", package="melting5jars"))
require(melting5jars)
melting <- new(J("melting.Main"))
optionManager <- new(J("melting.configuration.OptionManagement"))
results <- melting$getMeltingResults(opts, optionManager)
calculMethod <- results$getCalculMethod()
enthalpy_cal <- results$getEnthalpy()
entropy_cal <- results$getEntropy()
enthalpy_J <- entropy_J <- NULL
if (.jinstanceof(calculMethod, J("melting.nearestNeighborModel.NearestNeighborMode"))) {
enthalpy_J <- results$getEnergyValueInJ(enthalpy_cal)
entropy_J <- results$getEnergyValueInJ(entropy_cal)
}
melting_temp_C <- results$getTm()
list(
enthalpy_cal = enthalpy_cal,
entropy_cal = entropy_cal,
enthalpy_J = enthalpy_J,
entropy_J = entropy_J,
melting_temp_C = melting_temp_C
) -> out
class(out) <- c("melting_res")
out
}
That also has separate values for enthalpy and entropy depending on the method result.
We can also make a print helper function since we classed the list() we're returning:
print.melting_res <- function(x, ...) {
cat(
"The MELTING results are:\n\n",
" - Enthalpy: ", prettyNum(x$enthalpy_cal), " cal/mol",
{if (!is.null(x$enthalpy_J)) paste0(" (", prettyNum(x$enthalpy_J), " J /mol)", collapse="") else ""}, "\n",
" - Entropy: ", prettyNum(x$entropy_cal), " cal/mol-K",
{if (!is.null(x$entropy_J)) paste0(" (", prettyNum(x$entropy_J), " J /mol-K)", collapse="") else ""}, "\n",
" - Meltng temperature: ", prettyNum(x$melting_temp_C), " degress C\n",
sep=""
)
}
(I made an assumption you're used to seeing the MELTING 5 command line output)
And, finally, re-run the computation:
Sodium <- 0.05
opts <- c(
"-S", "GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTTCCAC",
"-H", "dnadna",
"-P", 5e-8,
"-E", paste("Na=", Sodium, sep = "")
)
res <- get_melting_results(opts)
res
## The MELTING results are:
##
## - Enthalpy: -408000 cal/mol (-1705440 J /mol)
## - Entropy: -1092.4 cal/mol-K (-4566.232 J /mol-K)
## - Meltng temperature: 72.04301 degress C
str(res)
## List of 5
## $ enthalpy_cal : num -408000
## $ entropy_cal : num -1092
## $ enthalpy_J : num -1705440
## $ entropy_J : num -4566
## $ melting_temp_C: num 72
## - attr(*, "class")= chr "melting_res"
You should be able to use the above methodology to wrap other components (if any) in the MELTING library.
For a university project I have to implement arules(package of R) in java. I have successfully integrated R and java using JRI. I did not understand how to get output of "inspect(Groceries[1:1])". I have tried with asString(),asString[]() but this gives me following error:
Exception in thread "main" java.lang.NullPointerException
at TestR.main(TestR.java:11)
Also, how can implement summary(Groceries) in java? How to get output of summary in String array or string?
R code:
>data(Groceries)
>inspect(Groceries[1:1])
>summary(Groceries)
Java code:
import org.rosuda.JRI.Rengine;
import org.rosuda.JRI.REXP;
public class TestR {
public static void main(String[] args){
Rengine re = new Rengine(new String[]{"--no-save"}, false, null);
re.eval("library(arules)");
re.eval("data(Groceries)");
REXP result = re.eval("inspect(Groceries[1:1])");
System.out.println(result.asString());
}
}
Appears that the inspect function in pkg:arules returns NULL. The output you see is a "side-effect". You can attempt to "capture output" but this is untested since I don't have experience with this integration across languages. Try instead.:
REXP result = re.eval("capture.output( inspect(Groceries[1:1]) )");
In an R console session you will get:
library(arules)
data("Adult")
rules <- apriori(Adult)
val <- inspect(rules[1000])
> str(val)
NULL
> val.co <- capture.output(inspect(rules[1000]))
> val.co
[1] " lhs rhs support confidence lift"
[2] "1 {education=Some-college, "
[3] " sex=Male, "
[4] " capital-loss=None} => {native-country=United-States} 0.1208181 0.9256471 1.031449"
But I haven't tested this in a non-interactive session. May need to muck with the file argument to capture.output, ... or it may not work at all.
So i'm trying to use RCaller to do the following (in psuedo-code):
x=simarray(..) // in java
'send x to R'
run y = rlogcon(40000, sort(x)) //in R, rlogcon is part of rlogcondens and the function
produces a numeric vector of length 40000
//send y to java and hold it in a double matrix.
this is what i've got in my main function (i've adapted one of the examples I found, but I must have made a mistake/misunderstood something. I tested the example on my machine, and it worked as expected):
RCaller caller = new RCaller();
RCode code = new RCode();
double[] x = a.simarraysimbeta(5, 1, 100, 30, 40); //some method
savesample("simarraysimbeta.txt",x); //testing, it works.
caller.setRscriptExecutable("C:\\Program Files\\R\\R-3.1.0\\bin\\Rscript.exe");
code.addDoubleArray("X", x);
code.addRCode("library(logcondens)"); //rlogcon is part of logcondens library
code.addRCode("ols <- rlogcon(40,000, sort(X))");
caller.setRCode(code);
caller.runAndReturnResult("ols");
double[] residuals = caller.getParser().getAsDoubleArray("X_star");
and the following relevent imports:
import rcaller.RCaller;
import rcaller.RCode;
import rcaller;
I get the following error:
Exception in thread "main" rcaller.exception.ParseException: Can not
handle R results due to : rcaller.exception.ParseException: Can not
parse output: The generated file
C:\Users\jo\AppData\Local\Temp\Routput8804446513483695061 is empty
here is the output:
concat<-function(to,...){
to<-paste(to,toString(...),sep="");
return(to);
}
cleanNames<-function(names){
cleanNames<-paste(unlist(strsplit(names,"\\.")),collapse="_");
Exception in thread "main" rcaller.exception.ParseException: Can not
handle R results due to : rcaller.exception.ParseException: Can not
parse output: The generated file
C:\Users\jo\AppData\Local\Temp\Routput8804446513483695061 is empty
cleanNames<-paste(unlist(strsplit(cleanNames,"<")),collapse="");
at rcaller.RCaller.runAndReturnResult(RCaller.java:409)
cleanNames<-paste(unlist(strsplit(cleanNames,">")),collapse="");
at dissertation.Dissertation.main(Dissertation.java:709)
cleanNames<-paste(unlist(strsplit(cleanNames," ")),collapse="");
cleanNames<-paste(unlist(strsplit(cleanNames,"\\(")),collapse="");
cleanNames<-paste(unlist(strsplit(cleanNames,"\\)")),collapse="");
cleanNames<-paste(unlist(strsplit(cleanNames,"\\[")),collapse="");
cleanNames<-paste(unlist(strsplit(cleanNames,"\\]")),collapse="");
cleanNames<-paste(unlist(strsplit(cleanNames,"\\*")),collapse="");
return(cleanNames);
}
makevectorxml<-function(code,objt,name=""){
xmlcode<-code;
if(name==""){
varname<-cleanNames(deparse(substitute(obj)));
}else{
varname<-name;
}
obj<-objt;
n <- 0; m <- 0
mydim <- dim(obj)
if(!is.null(mydim)){
n <- mydim[1]; m <- mydim[2];
}else{
n <- length(obj); m <- 1;
}
if(is.matrix(obj)) obj<-as.vector(obj);
if(typeof(obj)=="language") obj<-toString(obj);
if(typeof(obj)=="logical") obj<-as.character(obj);
if(is.vector(obj) && is.numeric(obj)){
xmlcode<-paste(xmlcode,"<variable name=\"",varname,"\" type=\"numeric\" n=\"", n, "\" m=\"", m, "\">",sep="");
for (i in obj){
xmlcode<-paste(xmlcode,"<v>",sep="");
xmlcode<-paste(xmlcode,toString(i),sep="");
xmlcode<-paste(xmlcode,"</v>",sep="");
}
xmlcode<-paste(xmlcode,"</variable>\n",sep="");
}
if(is.vector(obj) && is.character(obj)){
xmlcode<-paste(xmlcode,"<variable name=\"",varname,"\" type=\"character\">\n",sep="");
for (i in obj){
xmlcode<-paste(xmlcode,"<v>",sep="");
xmlcode<-paste(xmlcode,toString(i),sep="");
xmlcode<-paste(xmlcode,"</v>",sep="");
}
xmlcode<-paste(xmlcode,"</variable>\n");
}
return(xmlcode);
}
makexml<-function(obj,name=""){
xmlcode<-"<?xml version=\"1.0\"?>\n";
xmlcode<-concat(xmlcode,"<root>\n");
if(!is.list(obj)){
xmlcode<-makevectorxml(xmlcode,obj,name);
}
else{
objnames<-names(obj);
for (i in 1:length(obj)){
xmlcode<-makevectorxml(xmlcode,obj[[i]],cleanNames(objnames[[i]]));
}
}
xmlcode<-concat(xmlcode,"</root>\n");
return(xmlcode);
}
X<-c(##100 doubles);
library(logcondens)
ols <- rlogcon(40,000, sort(X))
cat(makexml(obj=ols, name="ols"), file="C:/Users/##/AppData/Local/Temp/Routput8804446513483695061")
40,000 shold be 40000 in your code.
There are two ways in which a file remains empty:
there is an error in R code
the result is NULL or NA
I recommend you to use tryCach in R
ols <- tryCatch({
rlogcon(40,000, sort(X))
}, error = function(e) {
-1
})
And at the end if ols equlas -1, you'll know that there was an error in R
I have this code :
import org.rosuda.REngine.Rserve.RConnection;
public class TestProgram {
public static void main(String[] args) {
try {
RConnection rConnection = new RConnection();
// make a new local connection on default port (6311)
rConnection.eval("for(i in 1:.Machine$integer.max){}");
System.out.println("Done!");
}
catch(Exception e) {
System.out.println(e.toString());
}
}
}
I get this exception :
org.rosuda.REngine.Rserve.RserveException: eval failed, request status: error code: 127
If I change :
rConnection.eval("for(i in 1:.Machine$integer.max){}");
to
rConnection.eval("for(i in 1:777){}");
it does work :-)
Does anyone know what's going on ?
P.S I started Rserve from R ( same machine ) using :
>library(Rserve)
>Rserve()
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rserve_1.7-3
loaded via a namespace (and not attached):
[1] tools_3.0.1
OS is Windows 8. I did not try this on Linux.
You should check the return from the eval function to see if it extends try-error. If it does then print it to debug string to get the error message. The section below was taken from the Rserve documentation. This will give you the error message that caused the 127. You should also probably use parseAndEval rather than just eval.
http://www.rforge.net/Rserve/faq.html
c.assign(".tmp.", myCode);
REXP r = c.parseAndEval("try(eval(parse(text=.tmp.)),silent=TRUE)");
if (r.inherits("try-error")) System.err.println("Error: "+r.toString())
else { // success .. }
You might also want to check this link in case it is a restriction of your R environment.
R - Big Data - vector exceeds vector length limit
EDIT: Fixing Chris Hinshaw's answer
c.assign(".tmp.", myCode);
REXP r = c.parseAndEval("try(eval(parse(text=.tmp.)),silent=TRUE)");
if (r.inherits("try-error")) System.err.println("Error: " + r.asString())
else { // success .. }
Note that the println should be using asString(), not toString()
I am trying to implement clustering using R in java by employing R caller. I am trying to run sample code for clustering validation and I get that common error faced by most of the users: Premature end of file
package test;
import rcaller.RCaller;
import java.io.File;
import java.lang.*;
import java.util.*;
import java.awt.image.DataBuffer;
public class test3 {
public static void main(String[] args) {
new test3();
}
public test3()
{
try{
RCaller caller = new RCaller();
caller.cleanRCode();
caller.setRscriptExecutable("C:/Program Files/R/R-2.15.1/bin/x64/Rscript");
caller.cleanRCode();
caller.addRCode("library(clvalid)");
caller.addRCode("data(mouse)");
caller.addRCode("express <- mouse [,c(M1,M2,M3,NC1,NC2,NC3)]");
caller.addRCode("rownames (express) <- mouse$ID ");
caller.addRCode("intern <- clValid(express, 2:6 , clMethods = c( hierarchical,kmeans,diana,clara,model) ,validation = internal)");
caller.addRCode("b <- summary(intern) ");
caller.runAndReturnResult("b");
}
catch (Exception e){
e.printStackTrace();
}
}
}
You have some spelling mistakes in you code. like clValid not clvalid , and you miss many quotes like "hierarchical",....
I think it is better to put your code in a script, and call it from java like this :
Runtime.getRuntime().exec("Rscript myScript.R");
where myScript.R is :
library(clValid)
data(mouse)
express <- mouse [,c('M1','M2','M3','NC1','NC2','NC3')]
rownames (express) <- mouse$ID
intern <- clValid(express, 2:6 , clMethods = c( 'hierarchical','kmeans',
'diana','clara','model') ,
validation = 'internal')
b <- summary(intern)