org.rosuda.REngine.REXPMismatchException Java Examples

/**
 * Get R command text output
 * 
 * @param command R command returning text
 * @return String
 */
public String asString(String command) {
  try {
    String s =
        silentlyEval("paste(capture.output(print(" + command + ")),collapse='\\n')").asString();
    return s;
  } catch (REXPMismatchException ex) {
    return ex.getMessage();
  }
  /*
   * String[] lines = null; try { lines = silentlyEval("capture.output( " + command +
   * ")").asStrings(); } catch (REXPMismatchException e) { return e.getMessage(); } if (lines ==
   * null) { return ""; } StringBuffer sb = new StringBuffer(); for (String l : lines) {
   * sb.append(l); sb.append("\n"); } return sb.toString();
   */
}
 

public static String cat(RList list) {
  try {
    StringBuffer sb = new StringBuffer("\t");
    double[][] data = new double[list.names.size()][];
    for (int i = 0; i < list.size(); i++) {
      String n = list.keyAt(i);
      sb.append(n + "\t");
      data[i] = list.at(n).asDoubles();
    }
    sb.append("\n");
    for (int i = 0; i < data[0].length; i++) {
      sb.append((i + 1) + "\t");
      for (int j = 0; j < data.length; j++) {
        sb.append(data[j][i] + "\t");
      }
      sb.append("\n");
    }
    return sb.toString();
  } catch (REXPMismatchException r) {
    return "(Not a numeric dataframe)\n" + new REXPList(list).toDebugString();
  }
}
 

/**
 * @return available R commands
 */
public String[] listCommands() {
  silentlyEval(
      ".keyWords <- function() {n <- length(search());result <- c();for (i in 1:n) {result <- c(result,ls(pos=i,all.names=TRUE))}; result}");
  REXP rexp = silentlyEval(".keyWords()");
  String as[] = null;
  try {
    if (rexp != null && (as = rexp.asStrings()) != null) {
      return as;
    } else {
      return null;
    }
  } catch (REXPMismatchException ex) {
    log(HEAD_ERROR + ex.getMessage() + "\n  listCommands()", Level.ERROR);
    return null;
  }
}
 

/**
 * Check for package loaded in R environment.
 * 
 * @param pack R package name
 * @return package loading status
 */
public boolean isPackageLoaded(String pack) {
  silentlyVoidEval(loadedpacks + "<-.packages()", false);
  boolean isloaded = false;
  try {
    REXP i = silentlyEval("is.element(set=" + loadedpacks + ",el='" + pack + "')");
    if (i != null) {
      isloaded = i.asInteger() == 1;
    }
  } catch (REXPMismatchException ex) {
    log(HEAD_ERROR + ex.getMessage() + "\n  isPackageLoaded(String pack=" + pack + ")",
        Level.ERROR);
  }
  if (isloaded) {
    log(_PACKAGE_ + pack + " is loaded.", Level.INFO);
  } else {
    log(_PACKAGE_ + pack + " is not loaded.", Level.INFO);
  }

  // silentlyEval("rm(" + loadedpacks + ")");
  return isloaded;
}
 

/**
 * Prepare REngine and user workspace environmet
 *
 * @param dataminingInstance
 * @param userProfile
 * @throws IOException
 * @throws REXPMismatchException
 * @throws REngineException
 * @throws NamingException
 */
private void setupEnvonmentForExternal() throws IOException, REngineException, REXPMismatchException, NamingException {
	logger.debug("IN");
	// new R-engine
	re = createREngineInstanceWithWork();
	if (re == null) {
		logger.error("Cannot load R");
		return;
	}
	re.parseAndEval("setwd(\"" + DataMiningUtils.UPLOADED_FILE_PATH + DataMiningConstants.DATA_MINING_EXTERNAL_CODE_PATH + "\")");
	logger.debug("Set working directory");
	// commandsExecutor.setRe(re);
	datasetsExecutor.setRe(re);
	outputExecutor.setRe(re);
	scriptExecutor.setRe(re);
	fileExecutor.setRe(re);

	logger.debug("OUT");
}
 

protected void updateDataset(DataMiningDataset ds) throws IOException, REngineException, REXPMismatchException {
	logger.debug("IN");
	File fileDSDir = new File(DataMiningUtils.getUserResourcesPath(profile) + ds.getName());
	// /find file in dir
	File[] dsfiles = fileDSDir.listFiles();
	if (dsfiles != null) {
		String fileDSPath = dsfiles[0].getPath();

		fileDSPath = fileDSPath.replaceAll("\\\\", "/");
		logger.debug("File ds path " + fileDSPath);

		String stringToEval = null;
		if (ds.getSubstituteLabel() != null && ds.getSubstituteLabel() != "") // functionsCatalog executeWithNewData
		{
			stringToEval = ds.getSubstituteLabel() + "<-read." + ds.getReadType() + "(\"" + fileDSPath + "\"," + ds.getOptions() + ");";
		} else // dataminingEngine e functionsCatalog executeDemo
		{
			stringToEval = ds.getName() + "<-read." + ds.getReadType() + "(\"" + fileDSPath + "\"," + ds.getOptions() + ");";

		}
		logger.debug("R code to eval " + stringToEval);
		re.parseAndEval(stringToEval);
	}
	logger.debug("OUT");
}
 

/**
 * 
 * @param robject R object name
 * @return R type of object
 */
public String typeOf(String robject) {
  if (robject == null) {
    return "NULL";
  }
  for (String t : types) {
    REXP is = silentlyEval("is." + t + "(" + robject + ")");
    try {
      if (is != null && is.asInteger() == 1) {
        return t;
      }
    } catch (REXPMismatchException ex) {
      log(HEAD_ERROR + "[typeOf] " + robject + " type unknown.", Level.ERROR);
      return null;
    }
  }
  return "unknown";
}
 

/**
 * Set R list in R env.
 * 
 * @param varname R list name
 * @param data numeric data in list
 * @param names names of columns
 */
public boolean set(String varname, double[][] data, String... names) {
  RList list = buildRList(data, names);
  log(HEAD_SET + varname + " <- " + toString(list), Level.INFO);
  try {
    synchronized (connection) {
      connection.assign(varname, REXP.createDataFrame(list));
    }
  } catch (REXPMismatchException re) {
    log(HEAD_ERROR + " RList " + list.toString() + " not convertible as dataframe.", Level.ERROR);
    return false;
  } catch (RserveException ex) {
    log(HEAD_EXCEPTION + ex.getMessage() + "\n  set(String varname=" + varname
        + ",double[][] data, String... names)", Level.ERROR);
    return false;
  }
  return true;
}
 

protected String evalFilesNeeded(HashMap paramsFilled) throws IOException, REngineException, REXPMismatchException {
	logger.debug("IN");
	if (re != null && dataminingInstance.getFiles() != null && !dataminingInstance.getFiles().isEmpty()) {
		for (Iterator fIt = dataminingInstance.getFiles().iterator(); fIt.hasNext();) {
			DataMiningFile f = (DataMiningFile) fIt.next();

			// Save file
			String strPathUploadedFile = DataMiningUtils.getUserResourcesPath(profile) + f.getFileName();
			File file = new File(strPathUploadedFile);
			BufferedOutputStream writer = new BufferedOutputStream(new FileOutputStream(file));
			writer.write(f.getContent());
			writer.flush();
			writer.close();

			// put file path into variable
			String stringToEval = f.getAlias() + "='" + strPathUploadedFile + "'\n";
			re.parseAndEval(stringToEval);

		}
	}
	logger.debug("OUT");
	return "";
}
 

/**
 * Get R command text output
 * 
 * @param command R command returning text
 * @return String
 */
public String asString(String command) {
  try {
    String s =
        silentlyEval("paste(capture.output(print(" + command + ")),collapse='\\n')").asString();
    return s;
  } catch (REXPMismatchException ex) {
    return ex.getMessage();
  }
  /*
   * String[] lines = null; try { lines = silentlyEval("capture.output( " + command +
   * ")").asStrings(); } catch (REXPMismatchException e) { return e.getMessage(); } if (lines ==
   * null) { return ""; } StringBuffer sb = new StringBuffer(); for (String l : lines) {
   * sb.append(l); sb.append("\n"); } return sb.toString();
   */
}
 

/**
 * Set R list in R env.
 * 
 * @param varname R list name
 * @param data numeric data in list
 * @param names names of columns
 */
public boolean set(String varname, double[][] data, String... names) {
  RList list = buildRList(data, names);
  log(HEAD_SET + varname + " <- " + toString(list), Level.INFO);
  try {
    synchronized (connection) {
      connection.assign(varname, REXP.createDataFrame(list));
    }
  } catch (REXPMismatchException re) {
    log(HEAD_ERROR + " RList " + list.toString() + " not convertible as dataframe.", Level.ERROR);
    return false;
  } catch (RserveException ex) {
    log(HEAD_EXCEPTION + ex.getMessage() + "\n  set(String varname=" + varname
        + ",double[][] data, String... names)", Level.ERROR);
    return false;
  }
  return true;
}
 

/**
 * 
 * @param robject R object name
 * @return R type of object
 */
public String typeOf(String robject) {
  if (robject == null) {
    return "NULL";
  }
  for (String t : types) {
    REXP is = silentlyEval("is." + t + "(" + robject + ")");
    try {
      if (is != null && is.asInteger() == 1) {
        return t;
      }
    } catch (REXPMismatchException ex) {
      log(HEAD_ERROR + "[typeOf] " + robject + " type unknown.", Level.ERROR);
      return null;
    }
  }
  return "unknown";
}
 

/**
 * Wraps the execution of an arbitrary R expression. Both errors and results are logged.
 *
 * @param input
 *            The R expression to evaluate.
 *
 * @return The result or the error of the evaluation of the given R expression. The method tries to convert it into a string, if possible.
 */
public Object evalWithR(final String input) throws InvalidREvaluationResultException {
	Object out = null;

	try {
		out = this.rCon.eval(input);

		Object output = null;

		if (out instanceof REXPString) {
			output = ((REXPString) out).asString();
		} else if (out instanceof REXPLogical) {
			output = ((REXPLogical) out).toDebugString();
		} else if (out != null) {
			output = out;
		} else {
			throw new InvalidREvaluationResultException("Got a null result for evaluation input: \"" + input + "\"");
		}

		RBridgeControl.LOGGER.trace("> REXP: {} return: {}", input, output);
	} catch (final REXPMismatchException exc) {
		RBridgeControl.LOGGER.error("Error R expr.: {} Cause: {}", input, exc.getMessage(), exc);
	}

	return out;
}
 

/**
 * Check for package loaded in R environment.
 * 
 * @param pack R package name
 * @return package loading status
 */
public boolean isPackageLoaded(String pack) {
  silentlyVoidEval(loadedpacks + "<-.packages()", false);
  boolean isloaded = false;
  try {
    REXP i = silentlyEval("is.element(set=" + loadedpacks + ",el='" + pack + "')");
    if (i != null) {
      isloaded = i.asInteger() == 1;
    }
  } catch (REXPMismatchException ex) {
    log(HEAD_ERROR + ex.getMessage() + "\n  isPackageLoaded(String pack=" + pack + ")",
        Level.ERROR);
  }
  if (isloaded) {
    log(_PACKAGE_ + pack + " is loaded.", Level.INFO);
  } else {
    log(_PACKAGE_ + pack + " is not loaded.", Level.INFO);
  }

  // silentlyEval("rm(" + loadedpacks + ")");
  return isloaded;
}
 

/**
 * @return available R commands
 */
public String[] listCommands() {
  silentlyEval(
      ".keyWords <- function() {n <- length(search());result <- c();for (i in 1:n) {result <- c(result,ls(pos=i,all.names=TRUE))}; result}");
  REXP rexp = silentlyEval(".keyWords()");
  String as[] = null;
  try {
    if (rexp != null && (as = rexp.asStrings()) != null) {
      return as;
    } else {
      return null;
    }
  } catch (REXPMismatchException ex) {
    log(HEAD_ERROR + ex.getMessage() + "\n  listCommands()", Level.ERROR);
    return null;
  }
}
 

public static String cat(RList list) {
  try {
    StringBuffer sb = new StringBuffer("\t");
    double[][] data = new double[list.names.size()][];
    for (int i = 0; i < list.size(); i++) {
      String n = list.keyAt(i);
      sb.append(n + "\t");
      data[i] = list.at(n).asDoubles();
    }
    sb.append("\n");
    for (int i = 0; i < data[0].length; i++) {
      sb.append((i + 1) + "\t");
      for (int j = 0; j < data.length; j++) {
        sb.append(data[j][i] + "\t");
      }
      sb.append("\n");
    }
    return sb.toString();
  } catch (REXPMismatchException r) {
    return "(Not a numeric dataframe)\n" + new REXPList(list).toDebugString();
  }
}
 

/**
 * Test for {@link RserveMeanIntegrationTest#mean(int[])}.
 * 
 * @throws REXPMismatchException if an error occurs
 * @throws REngineException      if an error occurs
 */
@Test
public void givenValues_whenMean_thenCorrect() throws REngineException, REXPMismatchException {
    int[] input = { 1, 2, 3, 4, 5 };
    double result = rserveMean.mean(input);
    Assert.assertEquals(3.0, result, 0.000001);
}
 

/**
 * Get R command text output in HTML format
 * 
 * @param command R command returning text
 * @return HTML string
 */
public String asR2HTML(String command) {
  String ret = installPackage("R2HTML", true);
  if (!ret.equals(PACKAGEINSTALLED)) {
    return ret;
  }
  int h = Math.abs(command.hashCode());
  silentlyEval("HTML(file=\"htmlfile_" + h + "\", " + command + ")");
  String[] lines = null;
  try {
    lines = silentlyEval("readLines(\"htmlfile_" + h + "\")").asStrings();
  } catch (REXPMismatchException e) {
    return e.getMessage();
  }
  removeFile("htmlfile_" + h);
  if (lines == null) {
    return "";
  }

  StringBuffer sb = new StringBuffer();
  for (String l : lines) {
    sb.append(l);
    sb.append("\n");
  }
  String str = sb.toString();
  str = str.replace("align= center ", "align='center'");
  str = str.replace("cellspacing=0", "cellspacing='0'");
  str = str.replace("border=1", "border='1'");
  str = str.replace("align=bottom", "align='bottom'");
  str = str.replace("class=dataframe", "class='dataframe'");
  str = str.replace("class= firstline ", "class='firstline'");
  str = str.replace("class=firstcolumn", "class='firstcolumn'");
  str = str.replace("class=cellinside", "class='cellinside'");
  str = str.replace("border=0", "border='0'");
  str = str.replace("class=captiondataframe", "class='captiondataframe'");
  str = str.replace("</td></table>", "</td></tr></table>");
  return str;
}
 

public String getRServeOS() {
  try {
    return eval("Sys.info()['sysname']", TRY_MODE).asString();
  } catch (REXPMismatchException re) {
    return "unknown";
  }
}
 

public void update() {
  try {
    if (R == null) {
      ls = new String[0];
    } else {
      REXP rls = R.silentlyEval("ls()");
      if (rls != null) {
        ls = rls.asStrings();
      } else {
        ls = new String[0];
      }
    }
    if (ls != null && ls.length > 0) {
      for (String l : ls) {
        try {
          // System.err.println("print(" + l + ")"+" -> ");
          String print = R.asHTML(l);// toHTML(R.silentlyEval("paste(capture.output(print("
                                     // + l +
                                     // ")),collapse='\\n')").asString());
          // String print = Rsession.cat(R.silentlyEval("print(" +
          // l + ")").asStrings());
          // System.err.println(" "+print);
          prints.put(l, print);
        } catch (Exception re) {
          prints.put(l, "?:" + re.getMessage());
        }
      }
    }
    EventQueue.invokeLater(new Runnable() {

      public void run() {
        _model.fireTableDataChanged();
      }
    });
  } catch (REXPMismatchException ex) {
    ex.printStackTrace();
  }
}
 

private void loadLibrariesFromRLocal(String libraryNames) throws REngineException, REXPMismatchException {
	logger.debug("IN");
	if (this.re != null) {
		re.parseAndEval("installed_packages = rownames(installed.packages())");
		REXP rHome = re.parseAndEval("try(libdir<-paste(R.home(),\"library\", sep=\"/\"))");
		if (!rHome.inherits("try-error") && !rHome.isNull()) {
			if (libraryNames != null && !libraryNames.isEmpty()) {
				setRProxy();
				String[] libs = libraryNames.split(",");
				for (int i = 0; i < libs.length; i++) {
					String lib = libs[i].trim();
					if (!lib.isEmpty()) {
						// check if the library is present in the workspace, if not try to install that package
						REXP libIsPresent = re.parseAndEval("\"" + lib + "\" %in% installed_packages");
						if (libIsPresent.isNull() || libIsPresent.asString().equalsIgnoreCase("false")) {
							// re.parseAndEval("try(install.packages(\"" + lib + "\",destdir=libdir))");
							logger.error("Libray '" + lib + "' is not present. Please, install the library in R before");
						}
						REXP rLibrary = re.parseAndEval("library(" + lib + ",lib.loc=libdir)");
						if (rLibrary.inherits("try-error")) {
							logger.error("Impossible to load library: " + lib);
						}
					}
				}
			}
		}
	}
	logger.debug("OUT");
}
 

protected boolean getAndEvalDefaultDataset(DataMiningDataset ds) throws IOException, REngineException, REXPMismatchException {
	logger.debug("IN");
	// checks relative path
	String relPathToDefDS = ds.getDefaultDS();
	if (relPathToDefDS == null || relPathToDefDS.equals("")) {
		return false;
	}
	if (relPathToDefDS.startsWith("/") || relPathToDefDS.startsWith("\\\\")) {
		relPathToDefDS = relPathToDefDS.substring(1);
	}
	String defDSRelPath = DataMiningUtils.UPLOADED_FILE_PATH + relPathToDefDS;

	defDSRelPath = defDSRelPath.replaceAll("\\\\", "/");
	logger.debug("Default path " + defDSRelPath);
	File fileDSDefault = new File(defDSRelPath);
	if (!fileDSDefault.exists()) {
		logger.debug("Default file doesn't exist");
		return false;
	}
	String stringToEval = ds.getName() + "<-read." + ds.getReadType() + "(\"" + defDSRelPath + "\"," + ds.getOptions() + ");";

	logger.debug("R code to eval " + stringToEval);
	re.parseAndEval(stringToEval);
	logger.debug("OUT");
	return true;

}
 

private void setupEnvonmentForExternal() throws IOException, REngineException, REXPMismatchException, NamingException {
	logger.debug("IN");

	String str = "" + DataMiningUtils.UPLOADED_FILE_PATH + DataMiningConstants.DATA_MINING_EXTERNAL_CODE_PATH;
	if (!PyLib.isPythonRunning()) {
		PyLib.startPython();
	}
	PyLib.execScript("import os\n" + "os.chdir(r'" + str + "')\n");

	logger.debug("Set working directory");
	logger.debug("OUT");
}
 

/**
 * Get R command text output in HTML format
 * 
 * @param command R command returning text
 * @return HTML string
 */
public String asR2HTML(String command) {
  String ret = installPackage("R2HTML", true);
  if (!ret.equals(PACKAGEINSTALLED)) {
    return ret;
  }
  int h = Math.abs(command.hashCode());
  silentlyEval("HTML(file=\"htmlfile_" + h + "\", " + command + ")");
  String[] lines = null;
  try {
    lines = silentlyEval("readLines(\"htmlfile_" + h + "\")").asStrings();
  } catch (REXPMismatchException e) {
    return e.getMessage();
  }
  removeFile("htmlfile_" + h);
  if (lines == null) {
    return "";
  }

  StringBuffer sb = new StringBuffer();
  for (String l : lines) {
    sb.append(l);
    sb.append("\n");
  }
  String str = sb.toString();
  str = str.replace("align= center ", "align='center'");
  str = str.replace("cellspacing=0", "cellspacing='0'");
  str = str.replace("border=1", "border='1'");
  str = str.replace("align=bottom", "align='bottom'");
  str = str.replace("class=dataframe", "class='dataframe'");
  str = str.replace("class= firstline ", "class='firstline'");
  str = str.replace("class=firstcolumn", "class='firstcolumn'");
  str = str.replace("class=cellinside", "class='cellinside'");
  str = str.replace("border=0", "border='0'");
  str = str.replace("class=captiondataframe", "class='captiondataframe'");
  str = str.replace("</td></table>", "</td></tr></table>");
  return str;
}
 

public String getRServeOS() {
  try {
    return eval("Sys.info()['sysname']", TRY_MODE).asString();
  } catch (REXPMismatchException re) {
    return "unknown";
  }
}
 

public void loadPackage(String packageName) throws RSessionWrapperException {

    String loadCode = "library(" + packageName + ", logical.return = TRUE)";

    if (TRY_MODE)
      loadCode = "try(" + loadCode + ", silent=TRUE)";

    String errorMsg = "The \"" + this.callerFeatureName + "\" requires " + "the \"" + packageName
        + "\" R package, which couldn't be loaded - is it installed in R?";

    if (this.rEngineType == REngineType.RSERVE) {

      if (this.session != null && !this.userCanceled) {
        LOG.log(logLvl, "Loading package '" + packageName + "'...");
        int loaded = 0;
        try {

          REXP r = ((RConnection) this.rEngine).eval(loadCode);
          if (r.inherits("try-error")) {
            LOG.severe("R Error [0]: " + r.asString());
            LOG.severe("R eval attempt [0]: " + loadCode);
          }
          loaded = r.asInteger();
          LOG.log(logLvl, "Load status: '" + (loaded != 0) + "'.");

        } catch (RserveException | REXPMismatchException e) {
          LOG.log(logLvl, "Loaded package KO: '" + e.getMessage() + "'.");
          // Remain silent if eval KO ("server down").
          loaded = Integer.MIN_VALUE;
        }

        // Throw loading failure only if eval OK, but return FALSE
        // (package not loaded).
        // ("server down" case will be handled soon enough).
        if (loaded == 0)
          if (!this.userCanceled)
            throw new RSessionWrapperException(errorMsg);

        LOG.log(logLvl, "Loaded package: '" + packageName + "'.");
      }

    } else { // RCaller

      ((RCaller) rEngine).getRCode().addRCode(loadCode);
      // try {
      //
      // ((RCallerScriptEngine2) rEngine).eval(loadCode);
      // } catch (ScriptException e) {
      //
      // if (!this.userCanceled)
      // throw new RSessionWrapperException(errorMsg);
      // }

    }
  }
 

/**
 * cast R object in java object
 * 
 * @param eval REXP R object
 * @return java object
 * @throws org.rosuda.REngine.REXPMismatchException
 */
public static Object cast(REXP eval) throws REXPMismatchException {
  if (eval == null) {
    return null;
  }

  /*
   * int[] dim = eval.dim(); String dims = "["; if (dim == null) { dims = "NULL"; } else { for
   * (int i : dim) { dims += (i + " "); } dims += "]"; }
   * 
   * System.out.println(eval.toString() + "\n  isComplex=     " + (eval.isComplex() ? "TRUE" :
   * "    false") + "\n  isEnvironment= " + (eval.isEnvironment() ? "TRUE" : "    false") +
   * "\n  isExpression=  " + (eval.isExpression() ? "TRUE" : "    false") + "\n  isFactor=      "
   * + (eval.isFactor() ? "TRUE" : "    false") + "\n  isFactor=      " + (eval.isFactor() ?
   * "TRUE" : "    false") + "\n  isInteger=     " + (eval.isInteger() ? "TRUE" : "    false") +
   * "\n  isLanguage=    " + (eval.isLanguage() ? "TRUE" : "    false") + "\n  isList=        " +
   * (eval.isList() ? "TRUE" : "    false") + "\n  isLogical=     " + (eval.isLogical() ? "TRUE" :
   * "    false") + "\n  isNull=        " + (eval.isNull() ? "TRUE" : "    false") +
   * "\n  isNumeric=     " + (eval.isNumeric() ? "TRUE" : "    false") + "\n  isRaw=         " +
   * (eval.isRaw() ? "TRUE" : "    false") + "\n  isRecursive=   " + (eval.isRecursive() ? "TRUE"
   * : "    false") + "\n  isString=      " + (eval.isString() ? "TRUE" : "    false") +
   * "\n  isSymbol=      " + (eval.isSymbol() ? "TRUE" : "    false") + "\n  isVector=      " +
   * (eval.isVector() ? "TRUE" : "    false") + "\n  length=  " + (eval.length()) + "\n  dim=  " +
   * dims);
   */
  if (eval.isNumeric()) {
    if (eval.dim() == null || eval.dim().length == 1) {
      double[] array = eval.asDoubles();
      if (array.length == 0) {
        return null;
      }
      if (array.length == 1) {
        return array[0];
      }
      return array;
    } else {
      // System.err.println("eval.dim()="+eval.dim()+"="+cat(eval.dim()));
      double[][] mat = eval.asDoubleMatrix();
      if (mat.length == 0) {
        return null;
      } else if (mat.length == 1) {
        if (mat[0].length == 0) {
          return null;
        } else if (mat[0].length == 1) {
          return mat[0][0];
        } else {
          return mat[0];
        }
      } else {
        if (mat[0].length == 0) {
          return null;
        } else if (mat[0].length == 1) {
          double[] dmat = new double[mat.length];
          for (int i = 0; i < dmat.length; i++) {
            dmat[i] = mat[i][0];
          }
          return dmat;
        } else {
          return mat;
        }
      }
    }
  }

  if (eval.isString()) {
    String[] s = eval.asStrings();
    if (s.length == 1) {
      return s[0];
    } else {
      return s;
    }
  }

  if (eval.isLogical()) {
    return eval.asInteger() == 1;
  }

  if (eval.isList()) {
    return eval.asList();
  }

  if (eval.isNull()) {
    return null;
  } else {
    System.err.println("Unsupported type: " + eval.toDebugString());
  }
  return eval.toString();
}
 

/**
 * cast R object in java object
 * 
 * @param eval REXP R object
 * @return java object
 * @throws org.rosuda.REngine.REXPMismatchException
 */
public static Object cast(REXP eval) throws REXPMismatchException {
  if (eval == null) {
    return null;
  }

  /*
   * int[] dim = eval.dim(); String dims = "["; if (dim == null) { dims = "NULL"; } else { for
   * (int i : dim) { dims += (i + " "); } dims += "]"; }
   * 
   * System.out.println(eval.toString() + "\n  isComplex=     " + (eval.isComplex() ? "TRUE" :
   * "    false") + "\n  isEnvironment= " + (eval.isEnvironment() ? "TRUE" : "    false") +
   * "\n  isExpression=  " + (eval.isExpression() ? "TRUE" : "    false") + "\n  isFactor=      "
   * + (eval.isFactor() ? "TRUE" : "    false") + "\n  isFactor=      " + (eval.isFactor() ?
   * "TRUE" : "    false") + "\n  isInteger=     " + (eval.isInteger() ? "TRUE" : "    false") +
   * "\n  isLanguage=    " + (eval.isLanguage() ? "TRUE" : "    false") + "\n  isList=        " +
   * (eval.isList() ? "TRUE" : "    false") + "\n  isLogical=     " + (eval.isLogical() ? "TRUE" :
   * "    false") + "\n  isNull=        " + (eval.isNull() ? "TRUE" : "    false") +
   * "\n  isNumeric=     " + (eval.isNumeric() ? "TRUE" : "    false") + "\n  isRaw=         " +
   * (eval.isRaw() ? "TRUE" : "    false") + "\n  isRecursive=   " + (eval.isRecursive() ? "TRUE"
   * : "    false") + "\n  isString=      " + (eval.isString() ? "TRUE" : "    false") +
   * "\n  isSymbol=      " + (eval.isSymbol() ? "TRUE" : "    false") + "\n  isVector=      " +
   * (eval.isVector() ? "TRUE" : "    false") + "\n  length=  " + (eval.length()) + "\n  dim=  " +
   * dims);
   */
  if (eval.isNumeric()) {
    if (eval.dim() == null || eval.dim().length == 1) {
      double[] array = eval.asDoubles();
      if (array.length == 0) {
        return null;
      }
      if (array.length == 1) {
        return array[0];
      }
      return array;
    } else {
      // System.err.println("eval.dim()="+eval.dim()+"="+cat(eval.dim()));
      double[][] mat = eval.asDoubleMatrix();
      if (mat.length == 0) {
        return null;
      } else if (mat.length == 1) {
        if (mat[0].length == 0) {
          return null;
        } else if (mat[0].length == 1) {
          return mat[0][0];
        } else {
          return mat[0];
        }
      } else {
        if (mat[0].length == 0) {
          return null;
        } else if (mat[0].length == 1) {
          double[] dmat = new double[mat.length];
          for (int i = 0; i < dmat.length; i++) {
            dmat[i] = mat[i][0];
          }
          return dmat;
        } else {
          return mat;
        }
      }
    }
  }

  if (eval.isString()) {
    String[] s = eval.asStrings();
    if (s.length == 1) {
      return s[0];
    } else {
      return s;
    }
  }

  if (eval.isLogical()) {
    return eval.asInteger() == 1;
  }

  if (eval.isList()) {
    return eval.asList();
  }

  if (eval.isNull()) {
    return null;
  } else {
    System.err.println("Unsupported type: " + eval.toDebugString());
  }
  return eval.toString();
}
 

public void loadPackage(String packageName) throws RSessionWrapperException {

    String loadCode = "library(" + packageName + ", logical.return = TRUE)";

    if (TRY_MODE)
      loadCode = "try(" + loadCode + ", silent=TRUE)";

    String errorMsg = "The \"" + this.callerFeatureName + "\" requires " + "the \"" + packageName
        + "\" R package, which couldn't be loaded - is it installed in R?";

    if (this.rEngineType == REngineType.RSERVE) {

      if (this.session != null && !this.userCanceled) {
        logger.log(logLvl, "Loading package '" + packageName + "'...");
        int loaded = 0;
        try {

          REXP r = ((RConnection) this.rEngine).eval(loadCode);
          if (r.inherits("try-error")) {
            logger.severe("R Error [0]: " + r.asString());
            logger.severe("R eval attempt [0]: " + loadCode);
          }
          loaded = r.asInteger();
          logger.log(logLvl, "Load status: '" + (loaded != 0) + "'.");

        } catch (RserveException | REXPMismatchException e) {
          logger.log(logLvl, "Loaded package KO: '" + e.getMessage() + "'.");
          // Remain silent if eval KO ("server down").
          loaded = Integer.MIN_VALUE;
        }

        // Throw loading failure only if eval OK, but return FALSE
        // (package not loaded).
        // ("server down" case will be handled soon enough).
        if (loaded == 0)
          if (!this.userCanceled)
            throw new RSessionWrapperException(errorMsg);

        logger.log(logLvl, "Loaded package: '" + packageName + "'.");
      }

    } else { // RCaller

      ((RCaller) rEngine).getRCode().addRCode(loadCode);
      // try {
      //
      // ((RCallerScriptEngine2) rEngine).eval(loadCode);
      // } catch (ScriptException e) {
      //
      // if (!this.userCanceled)
      // throw new RSessionWrapperException(errorMsg);
      // }

    }
  }
 

/**
 * Connects to the Rserve istance listening on 127.0.0.1:6311 and invokes the
 * customMean R function passing the given values as arguments.
 * 
 * @param values the input to the mean script
 * @return the result of the R script
 * @throws REngineException      if any error occurs
 * @throws REXPMismatchException if any error occurs
 */
public double mean(int[] values) throws REngineException, REXPMismatchException {
    RConnection c = new RConnection();
    c.assign("input", values);
    return c.eval("customMean(input)")
        .asDouble();
}