org.rosuda.REngine.REXP Java Examples

/**
 * @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;
}
 

/**
 * 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";
}
 

/**
 * Launch R command and return value.
 * 
 * @param expression R expresison to evaluate
 * @param tryEval encapsulate command in try() to cacth errors
 * @return REXP R expression
 */
public REXP eval(String expression, boolean tryEval) {
  // GLG HACK: Less verbosity when no error.
  // log(HEAD_EVAL + (tryEval ? HEAD_TRY : "") + expression, Level.INFO);

  REXP e = silentlyEval(expression, tryEval);

  for (UpdateObjectsListener b : updateObjects) {
    b.update();
  }

  // GLG HACK: Less verbosity when no error.
  // if (e != null) {
  // log(__ + e.toDebugString(), Level.INFO);
  // }

  return e;
}
 

/**
 * Launch R command and return value.
 * 
 * @param expression R expresison to evaluate
 * @param tryEval encapsulate command in try() to cacth errors
 * @return REXP R expression
 */
public REXP eval(String expression, boolean tryEval) {
  // GLG HACK: Less verbosity when no error.
  // log(HEAD_EVAL + (tryEval ? HEAD_TRY : "") + expression, Level.INFO);

  REXP e = silentlyEval(expression, tryEval);

  for (UpdateObjectsListener b : updateObjects) {
    b.update();
  }

  // GLG HACK: Less verbosity when no error.
  // if (e != null) {
  // log(__ + e.toDebugString(), Level.INFO);
  // }

  return e;
}
 

/**
 * 
 * @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;
}
 

/**
 * 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;
  }
}
 

/**
 * cast to java String representation of object
 * 
 * @param eval REXP R object
 * @return String representation
 */
public static String castToString(REXP eval) {
  if (eval == null) {
    return "";
  }
  return eval.toString();
}
 

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");
}
 

/**
 * cast to java String representation of object
 * 
 * @param eval REXP R object
 * @return String representation
 */
public static String castToString(REXP eval) {
  if (eval == null) {
    return "";
  }
  return eval.toString();
}
 

protected void evalScript(DataMiningCommand command, Boolean rerun, HashMap params) throws Exception {
	logger.debug("IN");

	if (re == null) {
		logger.error("No R instance found");
		return;
	}
	// checks whether executed before
	if (rerun || command.getExecuted() == null || !command.getExecuted()) {
		logger.debug("rerun or first execution");
		// load libraries from local dir (if needed)
		DataMiningScript script = getScript(command);
		loadLibrariesFromRLocal(script.getLibraries());
		logger.debug("loaded libraries from local dir (if needed)");
		// command-->script name --> execute script without output
		String scriptToExecute = getScriptCodeToEval(command, params);
		logger.debug("loaded script to execute: " + scriptToExecute);
		// loading libraries, preprocessing, functions definition in main
		// "auto"
		// script
		logger.info("creating temporary script...");

		String ret = createTemporarySourceScript(scriptToExecute);
		logger.info("created temporary script: " + ret);

		logger.info("executing temporary script...");
		REXP rexp = re.parseAndEval("source(\"" + ret + "\")");
		logger.info("temporary script execution completed");

		logger.debug("detects action to execute from command --> used to call functions");
		// detects action to execute from command --> used to call functions
		String action = command.getAction();
		if (action != null) {
			logger.info("evaluating action..");
			System.out.println("evaluating action..");
			re.parseAndEval(action);
			System.out.println("evaluated action");
			logger.info("evaluated action");
		}

		command.setExecuted(true);
		logger.debug("delete temporary scripts");
		deleteTemporarySourceScript(ret);
		logger.debug("deleted temporary scripts");
	} else {
		// everithing in user workspace
		logger.debug("Command " + command.getName() + " script " + command.getScriptName() + " already executed");
	}
	logger.debug("OUT");
}
 

private CreateDatasetResult createAndPersistDatasetProductByFunction(IEngUserProfile profile, String outVal, Output out, String function, String userId,
		String documentLabel) throws Exception {
	logger.debug("IN");
	CreateDatasetResult creationResult = new CreateDatasetResult();
	REXP rexp = null;
	DataMiningResult res = new DataMiningResult();

	FileDataSet dataSet = new FileDataSet();
	String path = getDatasetsDirectoryPath();
	String resourcePath = DAOConfig.getResourcePath();
	dataSet.setResourcePath(resourcePath);

	String spagoBiDatasetname = userId + "_" + documentLabel + "_" + out.getOuputLabel();
	JSONObject configurationObj = new JSONObject();

	configurationObj.put(DataSetConstants.FILE_TYPE, "CSV");
	configurationObj.put(DataSetConstants.CSV_FILE_DELIMITER_CHARACTER, ",");
	configurationObj.put(DataSetConstants.CSV_FILE_QUOTE_CHARACTER, "'");
	configurationObj.put(DataSetConstants.FILE_NAME, spagoBiDatasetname + ".csv");
	configurationObj.put("encoding", "UTF-8");
	configurationObj.put(DataSetConstants.XSL_FILE_SKIP_ROWS, DataSetConstants.XSL_FILE_SKIP_ROWS);
	configurationObj.put(DataSetConstants.XSL_FILE_LIMIT_ROWS, DataSetConstants.XSL_FILE_LIMIT_ROWS);
	configurationObj.put(DataSetConstants.XSL_FILE_SHEET_NUMBER, DataSetConstants.XSL_FILE_SHEET_NUMBER);

	String confString = configurationObj.toString();
	dataSet.setConfiguration(confString);

	String rExecution = "write.csv(" + outVal + ",file=" + path + spagoBiDatasetname + ",row.names=FALSE,na='')";
	rexp = re.parseAndEval("try(" + rExecution + ")");
	if (rexp.inherits("try-error")) {
		logger.debug("Script contains error(s)");
		creationResult.setRExecutionError(rexp.asString());
	}

	dataSet.setFileName(spagoBiDatasetname + ".csv");
	dataSet.setFileType("CSV");
	dataSet.setDsType(DataSetConstants.DS_FILE);

	String label = out.getOuputLabel();
	dataSet.setLabel(spagoBiDatasetname);
	dataSet.setName(spagoBiDatasetname);
	dataSet.setDescription("Dataset created from execution of document " + documentLabel + " by user " + userId);
	dataSet.setOwner(((UserProfile) profile).getUserId().toString());

	// ------------Metadata setting------------

	dataSet.loadData();
	IDataStore dataStore = dataSet.getDataStore();
	JSONArray metadataArray = new JSONArray();

	IMetaData metaData = dataStore.getMetaData();
	for (int i = 0; i < metaData.getFieldCount(); i++) {
		IFieldMetaData ifmd = metaData.getFieldMeta(i);
		for (int j = 0; j < metadataArray.length(); j++) {
			if (ifmd.getName().equals((metadataArray.getJSONObject(j)).getString("name"))) {
				if ("MEASURE".equals((metadataArray.getJSONObject(j)).getString("fieldType"))) {
					ifmd.setFieldType(IFieldMetaData.FieldType.MEASURE);
				} else {
					ifmd.setFieldType(IFieldMetaData.FieldType.ATTRIBUTE);
				}
				break;
			}
		}
	}
	IMetaData currentMetadata = dataStore.getMetaData();
	DatasetMetadataParser dsp = new DatasetMetadataParser();
	String dsMetadata = dsp.metadataToXML(currentMetadata);
	dataSet.setDsMetadata(dsMetadata);

	// ----------------------------------------

	IDataSetDAO dataSetDAO = DAOFactory.getDataSetDAO();
	dataSetDAO.setUserProfile(profile);

	logger.debug("check if dataset with label " + spagoBiDatasetname + " is already present");

	// check label is already present; insert or modify dependengly
	IDataSet iDataSet = dataSetDAO.loadDataSetByLabel(spagoBiDatasetname);

	// loadActiveDataSetByLabel(label);
	if (iDataSet != null) {
		logger.debug("a dataset with label " + spagoBiDatasetname + " is already present: modify it");
		dataSet.setId(iDataSet.getId());
		dataSetDAO.modifyDataSet(dataSet);
	} else {
		logger.debug("No dataset with label " + spagoBiDatasetname + " is already present: insert it");
		dataSetDAO.insertDataSet(dataSet);

	}
	creationResult.setDatasetlabel(spagoBiDatasetname);
	return creationResult;

}
 

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);
      // }

    }
  }
 

private CreateDatasetResult createAndPersistDataset(IEngUserProfile profile, String outVal, Output out, String userId, String documentLabel)
		throws Exception {
	logger.debug("IN");

	REXP rexp = null;
	CreateDatasetResult creationResult = new CreateDatasetResult();

	String spagoBiDatasetname = userId + "_" + documentLabel + "_" + out.getOuputLabel();

	FileDataSet dataSet = new FileDataSet();
	String path = getDatasetsDirectoryPath();
	String resourcePath = DAOConfig.getResourcePath();
	dataSet.setResourcePath(resourcePath);

	JSONObject configurationObj = new JSONObject();

	configurationObj.put(DataSetConstants.FILE_TYPE, "CSV");
	configurationObj.put(DataSetConstants.CSV_FILE_DELIMITER_CHARACTER, ",");
	configurationObj.put(DataSetConstants.CSV_FILE_QUOTE_CHARACTER, "\"");
	configurationObj.put(DataSetConstants.FILE_NAME, spagoBiDatasetname + ".csv");
	configurationObj.put(DataSetConstants.CSV_FILE_ENCODING, "UTF-8");
	configurationObj.put(DataSetConstants.XSL_FILE_SKIP_ROWS, DataSetConstants.XSL_FILE_SKIP_ROWS);
	configurationObj.put(DataSetConstants.XSL_FILE_LIMIT_ROWS, DataSetConstants.XSL_FILE_LIMIT_ROWS);
	configurationObj.put(DataSetConstants.XSL_FILE_SHEET_NUMBER, DataSetConstants.XSL_FILE_SHEET_NUMBER);

	String confString = configurationObj.toString();
	dataSet.setConfiguration(confString);

	String rExecution = "write.csv(" + outVal + ",file='" + path + "/" + spagoBiDatasetname + ".csv',row.names=FALSE,na='')";
	rexp = re.parseAndEval("try(" + rExecution + ")");
	if (rexp.inherits("try-error")) {
		logger.debug("Script contains error(s)");
		creationResult.setRExecutionError(rexp.asString());
	}

	dataSet.setFileName(spagoBiDatasetname + ".csv");
	dataSet.setFileType("CSV");
	dataSet.setDsType(DataSetConstants.DS_FILE);

	dataSet.setLabel(spagoBiDatasetname);
	dataSet.setName(spagoBiDatasetname);
	dataSet.setDescription("Dataset created from execution of document " + documentLabel + " by user " + userId);
	dataSet.setOwner(((UserProfile) profile).getUserId().toString());

	// ------------Metadata setting------------

	dataSet.loadData();
	IDataStore dataStore = dataSet.getDataStore();
	JSONArray metadataArray = new JSONArray();

	IMetaData metaData = dataStore.getMetaData();
	for (int i = 0; i < metaData.getFieldCount(); i++) {
		IFieldMetaData ifmd = metaData.getFieldMeta(i);
		for (int j = 0; j < metadataArray.length(); j++) {
			if (ifmd.getName().equals((metadataArray.getJSONObject(j)).getString("name"))) {
				if ("MEASURE".equals((metadataArray.getJSONObject(j)).getString("fieldType"))) {
					ifmd.setFieldType(IFieldMetaData.FieldType.MEASURE);
				} else {
					ifmd.setFieldType(IFieldMetaData.FieldType.ATTRIBUTE);
				}
				break;
			}
		}
	}
	IMetaData currentMetadata = dataStore.getMetaData();
	DatasetMetadataParser dsp = new DatasetMetadataParser();
	String dsMetadata = dsp.metadataToXML(currentMetadata);
	dataSet.setDsMetadata(dsMetadata);

	// ----------------------------------------

	IDataSetDAO dataSetDAO = DAOFactory.getDataSetDAO();
	dataSetDAO.setUserProfile(profile);

	logger.debug("check if dataset with label " + spagoBiDatasetname + " is already present");

	// check label is already present; insert or modify dependengly
	IDataSet iDataSet = dataSetDAO.loadDataSetByLabel(spagoBiDatasetname);

	// loadActiveDataSetByLabel(label);
	if (iDataSet != null) {
		logger.debug("a dataset with label " + spagoBiDatasetname + " is already present: modify it");
		dataSet.setId(iDataSet.getId());
		dataSetDAO.modifyDataSet(dataSet);
	} else {
		logger.debug("No dataset with label " + spagoBiDatasetname + " is already present: insert it");
		dataSetDAO.insertDataSet(dataSet);

	}
	creationResult.setDatasetlabel(spagoBiDatasetname);
	return creationResult;

}
 

/**
 * 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();
}
 

/**
 * Silently (ie no log) launch R command and return value.
 * 
 * @param expression R expression to evaluate
 * @param tryEval encapsulate command in try() to cacth errors
 * @return REXP R expression
 */
public REXP silentlyEval(String expression, boolean tryEval) {
  assert connected : "R environment not initialized.";
  if (expression == null) {
    return null;
  }
  if (expression.trim().length() == 0) {
    return null;
  }
  for (EvalListener b : eval) {
    b.eval(expression);
  }
  REXP e = null;
  try {
    synchronized (connection) {
      if (SINK_OUTPUT) {
        connection.parseAndEval("sink('" + SINK_FILE + "',type='output')");
      }
      if (tryEval) {
        e = connection.parseAndEval(
            "try(eval(parse(text='" + expression.replace("'", "\\'") + "')),silent=FALSE)");
      } else {
        e = connection.parseAndEval(expression);
      }
      if (SINK_OUTPUT) {
        connection.parseAndEval("sink(type='output')");
        try {
          lastOuput = connection
              .parseAndEval("paste(collapse='\n',readLines('" + SINK_FILE + "'))").asString();
          log(lastOuput, Level.OUTPUT);
        } catch (Exception ex) {
          lastOuput = ex.getMessage();
          log(lastOuput, Level.WARNING);
        }
        connection.parseAndEval("unlink('" + SINK_FILE + "')");
      }
    }
  } catch (Exception ex) {
    log(HEAD_EXCEPTION + ex.getMessage() + "\n  " + expression, Level.ERROR);
  }

  if (tryEval && e != null) {
    try {
      if (e.inherits("try-error")/*
                                  * e.isString() && e.asStrings().length > 0 && e.asString
                                  * ().toLowerCase().startsWith ("error")
                                  */) {
        log(HEAD_EXCEPTION + e.asString() + "\n  " + expression, Level.WARNING);
        e = null;
      }
    } catch (REXPMismatchException ex) {
      log(HEAD_ERROR + ex.getMessage() + "\n  " + expression, Level.ERROR);
      return null;
    }
  }
  return e;
}
 

/**
 * Silently (ie no log) launch R command and return value.
 * 
 * @param expression R expression to evaluate
 * @param tryEval encapsulate command in try() to cacth errors
 * @return REXP R expression
 */
public REXP silentlyEval(String expression, boolean tryEval) {
  assert connected : "R environment not initialized.";
  if (expression == null) {
    return null;
  }
  if (expression.trim().length() == 0) {
    return null;
  }
  for (EvalListener b : eval) {
    b.eval(expression);
  }
  REXP e = null;
  try {
    synchronized (connection) {
      if (SINK_OUTPUT) {
        connection.parseAndEval("sink('" + SINK_FILE + "',type='output')");
      }
      if (tryEval) {
        e = connection.parseAndEval(
            "try(eval(parse(text='" + expression.replace("'", "\\'") + "')),silent=FALSE)");
      } else {
        e = connection.parseAndEval(expression);
      }
      if (SINK_OUTPUT) {
        connection.parseAndEval("sink(type='output')");
        try {
          lastOuput = connection
              .parseAndEval("paste(collapse='\n',readLines('" + SINK_FILE + "'))").asString();
          log(lastOuput, Level.OUTPUT);
        } catch (Exception ex) {
          lastOuput = ex.getMessage();
          log(lastOuput, Level.WARNING);
        }
        connection.parseAndEval("unlink('" + SINK_FILE + "')");
      }
    }
  } catch (Exception ex) {
    log(HEAD_EXCEPTION + ex.getMessage() + "\n  " + expression, Level.ERROR);
  }

  if (tryEval && e != null) {
    try {
      if (e.inherits("try-error")/*
                                  * e.isString() && e.asStrings().length > 0 && e.asString
                                  * ().toLowerCase().startsWith ("error")
                                  */) {
        log(HEAD_EXCEPTION + e.asString() + "\n  " + expression, Level.WARNING);
        e = null;
      }
    } catch (REXPMismatchException ex) {
      log(HEAD_ERROR + ex.getMessage() + "\n  " + expression, Level.ERROR);
      return null;
    }
  }
  return e;
}
 

/**
 * 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);
      // }

    }
  }
 

/**
 * Silently (ie no log) launch R command and return value. Encapsulate command in try() to cacth
 * errors.
 * 
 * @param expression R expresison to evaluate
 * @return REXP R expression
 */
public REXP silentlyEval(String expression) {
  return silentlyEval(expression, TRY_MODE_DEFAULT);
}
 

/**
 * Launch R command and return value. Encapsulate command in try() to cacth errors.
 * 
 * @param expression R expresison to evaluate
 * @return REXP R expression
 */
public REXP eval(String expression) {
  return eval(expression, TRY_MODE_DEFAULT);
}
 

/**
 * Launch R command and return value. Encapsulate command in try() to cacth errors.
 * 
 * @param expression R expresison to evaluate
 * @return REXP R expression
 */
public REXP eval(String expression) {
  return eval(expression, TRY_MODE_DEFAULT);
}
 

/**
 * Silently (ie no log) launch R command and return value. Encapsulate command in try() to cacth
 * errors.
 * 
 * @param expression R expresison to evaluate
 * @return REXP R expression
 */
public REXP silentlyEval(String expression) {
  return silentlyEval(expression, TRY_MODE_DEFAULT);
}