- Nuiton-j2r-commits - mailman.cloud.codelutin.com

r245 - trunk
by tchemit＠users.nuiton.org Nov. 21, 2010

Nov. 21, 2010

Author: tchemit Date: 2010-11-21 15:30:33 +0100 (Sun, 21 Nov 2010) New Revision: 245 Url: http://nuiton.org/repositories/revision/nuiton-j2r/245 Log: Update mavenpom4redmineAndCentral to 2.4.1. Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-10-29 08:29:16 UTC (rev 244) +++ trunk/pom.xml 2010-11-21 14:30:33 UTC (rev 245) @@ -34,7 +34,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmineAndCentral</artifactId> - <version>2.4</version> + <version>2.4.1</version> </parent> <artifactId>nuiton-j2r</artifactId>

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r244 - trunk
by tchemit＠users.nuiton.org Oct. 29, 2010

Oct. 29, 2010

Author: tchemit Date: 2010-10-29 10:29:16 +0200 (Fri, 29 Oct 2010) New Revision: 244 Url: http://nuiton.org/repositories/revision/nuiton-j2r/244 Log: Update mavenpom4redmineAndCentral to 2.4. Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-10-26 12:57:28 UTC (rev 243) +++ trunk/pom.xml 2010-10-29 08:29:16 UTC (rev 244) @@ -34,7 +34,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmineAndCentral</artifactId> - <version>2.4-SNAPSHOT</version> + <version>2.4</version> </parent> <artifactId>nuiton-j2r</artifactId>

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r243 - trunk
by tchemit＠users.nuiton.org Oct. 26, 2010

Oct. 26, 2010

Author: tchemit Date: 2010-10-26 14:57:28 +0200 (Tue, 26 Oct 2010) New Revision: 243 Url: http://nuiton.org/repositories/revision/nuiton-j2r/243 Log: fix build (use inheritance from mavenpom for commons libs) Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-10-26 12:07:02 UTC (rev 242) +++ trunk/pom.xml 2010-10-26 12:57:28 UTC (rev 243) @@ -118,7 +118,6 @@ <dependency> <groupId>junit</groupId> <artifactId>junit</artifactId> - <scope>test</scope> </dependency>

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r242 - trunk
by tchemit＠users.nuiton.org Oct. 26, 2010

Oct. 26, 2010

Author: tchemit Date: 2010-10-26 14:07:02 +0200 (Tue, 26 Oct 2010) New Revision: 242 Url: http://nuiton.org/repositories/revision/nuiton-j2r/242 Log: use mavenpom 2.4-SNAPSHOT use camelCase style for version properties use default libraries version from mavenpom Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2010-10-22 08:51:00 UTC (rev 241) +++ trunk/pom.xml 2010-10-26 12:07:02 UTC (rev 242) @@ -34,7 +34,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmineAndCentral</artifactId> - <version>2.3.2</version> + <version>2.4-SNAPSHOT</version> </parent> <artifactId>nuiton-j2r</artifactId> @@ -92,7 +92,6 @@ <dependency> <groupId>commons-logging</groupId> <artifactId>commons-logging</artifactId> - <version>1.1.1</version> </dependency> <dependency> @@ -105,21 +104,20 @@ <dependency> <groupId>org.nuiton.thirdparty</groupId> <artifactId>REngine</artifactId> - <version>${rengine.version}</version> + <version>${rengineVersion}</version> <scope>compile</scope> </dependency> <dependency> <groupId>org.nuiton.thirdparty</groupId> <artifactId>Rserve</artifactId> - <version>${rengine.version}</version> + <version>${rengineVersion}</version> <scope>compile</scope> </dependency> <dependency> <groupId>junit</groupId> <artifactId>junit</artifactId> - <version>4.8.1</version> <scope>test</scope> </dependency> @@ -145,7 +143,7 @@ <properties> - <rengine.version>0.6-1</rengine.version> + <rengineVersion>0.6-1</rengineVersion>   @@ -165,7 +163,7 @@ <dependency> <groupId>org.nuiton.jrst</groupId> <artifactId>doxia-module-jrst</artifactId> - <version>${jrst.version}</version> + <version>${jrstPluginVersion}</version> </dependency> </dependencies> </plugin>

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r241 - in trunk/src: main/java/org/nuiton/j2r main/java/org/nuiton/j2r/types site/rst test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org Oct. 22, 2010

Oct. 22, 2010

Author: jcouteau Date: 2010-10-22 10:51:00 +0200 (Fri, 22 Oct 2010) New Revision: 241 Url: http://nuiton.org/repositories/revision/nuiton-j2r/241 Log: Improve code : use string builders, close streams in finally blocks, replace private by protected Modified: trunk/src/main/java/org/nuiton/j2r/REngine.java trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java trunk/src/main/java/org/nuiton/j2r/types/RList.java trunk/src/site/rst/installTest.rst trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java trunk/src/test/java/org/nuiton/j2r/NetTest.java Modified: trunk/src/main/java/org/nuiton/j2r/REngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/REngine.java 2010-10-19 15:12:39 UTC (rev 240) +++ trunk/src/main/java/org/nuiton/j2r/REngine.java 2010-10-22 08:51:00 UTC (rev 241) @@ -289,7 +289,7 @@ */ void saveRData(String filename) throws RException; - public void plot(String filename, String x, String y, String type, + void plot(String filename, String x, String y, String type, String main, String sub, String xlab, String ylab, String asp) throws RException; } //REngine Modified: trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java 2010-10-19 15:12:39 UTC (rev 240) +++ trunk/src/main/java/org/nuiton/j2r/REngineAbstract.java 2010-10-22 08:51:00 UTC (rev 241) @@ -39,7 +39,7 @@ * If true, commit each R instruction on the fly, if false, commit only when * the commit() method is called. */ - private Boolean autocommit = true; + protected Boolean autocommit = true; /** * Load a specific R session : @@ -343,45 +343,58 @@ eval("jpeg(\"" + filename + ".jpg\")"); - String Rinstruction = "plot("; + StringBuilder rinstruction = new StringBuilder("plot("); if ((x != null) && (!x.isEmpty())) { - Rinstruction += x; + rinstruction.append(x); } else { throw new IllegalArgumentException("x argument must be filled"); } if ((y != null) && (!y.isEmpty())) { - Rinstruction += ",y=" + y; + rinstruction.append(",y="); + rinstruction.append(y); } if (type != null) { - Rinstruction += ",type=\"" + type + "\""; + rinstruction.append(",type=\""); + rinstruction.append(type); + rinstruction.append("\""); } if (main != null) { - Rinstruction += ",main=\"" + main + "\""; + rinstruction.append(",main=\""); + rinstruction.append(main); + rinstruction.append("\""); } if (sub != null) { - Rinstruction += ",sub=\"" + sub + "\""; + rinstruction.append(",sub=\""); + rinstruction.append(sub); + rinstruction.append("\""); } if (xlab != null) { - Rinstruction += ",xlab=\"" + xlab + "\""; + rinstruction.append(",xlab=\""); + rinstruction.append(xlab); + rinstruction.append("\""); } if (ylab != null) { - Rinstruction += ",ylab=\"" + ylab + "\""; + rinstruction.append(",ylab=\""); + rinstruction.append(ylab); + rinstruction.append("\""); } if (asp != null) { - Rinstruction += ",asp=" + asp + "\""; + rinstruction.append(",asp="); + rinstruction.append(asp); + rinstruction.append("\""); } - Rinstruction += ")"; + rinstruction.append(")"); - eval(Rinstruction); + eval(rinstruction.toString()); eval("dev.off()"); } Modified: trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-10-19 15:12:39 UTC (rev 240) +++ trunk/src/main/java/org/nuiton/j2r/types/RDataFrame.java 2010-10-22 08:51:00 UTC (rev 241) @@ -273,15 +273,17 @@ this.rowNames = rowNames; //Create the r instruction (row.names(var)<-c("name 1",...,"name x")). - String rowNamesString = ""; + StringBuilder rowNamesString = new StringBuilder(); for (int i = 0; i < this.rowNames.size(); i++) { if (i != 0) { - rowNamesString += ","; + rowNamesString.append(","); } - rowNamesString += "\"" + rowNames.get(i) + "\""; + rowNamesString.append("\""); + rowNamesString.append(rowNames.get(i)); + rowNamesString.append("\""); } String rexp = String.format(RInstructions.SET_ROW_NAMES, - this.variable, rowNamesString); + this.variable, rowNamesString.toString()); //Send the r instruction to the engine. engine.voidEval(rexp); @@ -333,17 +335,21 @@ public String toRString() throws RException { checkVariable(); - String returnString = this.variable + "<-data.frame("; + StringBuilder returnString = new StringBuilder(); + returnString.append(this.variable); + returnString.append("<-data.frame("); + for (List<?> column:this.data){ if (!column.isEmpty()){ if (!(this.names.isEmpty())) { int index = this.data.indexOf(column); - returnString += this.names.get(index) + "=c("; + returnString.append(this.names.get(index)); + returnString.append("=c("); } else { - returnString += "c("; + returnString.append("c("); } Object firstElement = column.get(0); @@ -351,56 +357,62 @@ if (firstElement instanceof String) { for (Object obj:column) { - returnString += "\"" + obj + "\","; + returnString.append("\""); + returnString.append(obj); + returnString.append("\","); } } else if (firstElement instanceof Boolean) { for (Object obj:column) { if ((Boolean) obj) { - returnString += RInstructions.TRUE + ","; + returnString.append(RInstructions.TRUE + ","); } else { - returnString += RInstructions.FALSE + ","; + returnString.append(RInstructions.FALSE + ","); } } } else if (firstElement instanceof Integer) { for (Object obj:column) { - returnString += String.format(RInstructions.AS_INTEGER, - obj) + ","; + returnString.append( + String.format(RInstructions.AS_INTEGER,obj)); + returnString.append(","); } } else { for (Object obj:column) { - returnString += obj + ","; + returnString.append(obj); + returnString.append(","); } } - returnString = returnString.substring(0, - returnString.length() - 1); - returnString = returnString + "),"; + returnString = new StringBuilder(returnString.substring(0, + returnString.length() - 1)); + returnString.append("),"); } } if (!(this.rowNames.isEmpty())) { - returnString += "row.names=c("; + returnString.append("row.names=c("); for (String rowName : rowNames) { - returnString += "\"" + rowName + "\","; + returnString.append("\""); + returnString.append(rowName); + returnString.append("\","); } - returnString = - returnString.substring(0, returnString.length() - 1) + - "),stringsAsFactors=FALSE)"; + returnString = new StringBuilder(returnString.substring(0, returnString.length() - 1)); + returnString.append("),stringsAsFactors=FALSE)"); + } else if (this.data.isEmpty()) { - returnString += ")"; + returnString.append(")"); } else { - returnString += "stringsAsFactors=FALSE)"; + returnString.append("stringsAsFactors=FALSE)"); } if(log.isDebugEnabled()){ log.debug(returnString); } - return returnString; + return returnString.toString(); } /** @@ -656,28 +668,35 @@ */ public void exportCsv(File outputFile, boolean rowNames, boolean names) throws IOException { - BufferedWriter file = new BufferedWriter(new FileWriter(outputFile)); - if (names) { - if (rowNames) { - file.write(";"); + BufferedWriter file = null; + try { + file = new BufferedWriter(new FileWriter(outputFile)); + + if (names) { + if (rowNames) { + file.write(";"); + } + for (String name : this.names) { + file.write(name + ";"); + } + file.newLine(); } - for (String name : this.names) { - file.write(name + ";"); - } - file.newLine(); - } - for (int i = 0; i < this.data.get(0).size(); i++) { - if (rowNames) { - file.write(this.rowNames.get(i) + ";"); + for (int i = 0; i < this.data.get(0).size(); i++) { + if (rowNames) { + file.write(this.rowNames.get(i) + ";"); + } + for (List<?> aData : this.data) { + file.write(aData.get(i) + ";"); + } + file.newLine(); } - for (List<?> aData : this.data) { - file.write(aData.get(i) + ";"); + } finally { + if (file!=null){ + file.close(); } - file.newLine(); } - file.close(); } @@ -760,93 +779,100 @@ //temporary String to read lines. String tmp; + //temporary data list. + List<List<?>> tempData = new ArrayList<List<?>>(); + Integer dataSize; - //get the first line of the file - BufferedReader br = new BufferedReader(new FileReader(inputFile)); - tmp = br.readLine(); - String[] splitted = tmp.split(";"); + BufferedReader br = null; + try { + //get the first line of the file + br = new BufferedReader(new FileReader(inputFile)); + tmp = br.readLine(); + String[] splitted = tmp.split(";"); - //get the data size (number of columns) - if (rowNames) { - dataSize = splitted.length - 1; - } else { - dataSize = splitted.length; - } + //get the data size (number of columns) + if (rowNames) { + dataSize = splitted.length - 1; + } else { + dataSize = splitted.length; + } - //clear data, rowNames and names - this.data.clear(); - this.rowNames.clear(); - this.names.clear(); + //clear data, rowNames and names + this.data.clear(); + this.rowNames.clear(); + this.names.clear(); - if (names) { - //if names are present in the file, parse the first line to get - //the names. - this.names.addAll(Arrays.asList(splitted).subList(1, splitted.length)); - } + if (names) { + //if names are present in the file, parse the first line to get + //the names. + this.names.addAll(Arrays.asList(splitted).subList(1, splitted.length)); + } - //temporary data list. - List<List<?>> tempData = new ArrayList<List<?>>(); + //Initialize all the data columns with empty lists + for (int i = 0; i < dataSize; i++) { + List<Object> column = new ArrayList<Object>(); + tempData.add(column); + } - //Initialize all the data columns with empty lists - for (int i = 0; i < dataSize; i++) { - List<Object> column = new ArrayList<Object>(); - tempData.add(column); - } + while ((tmp = br.readLine()) != null) { - while ((tmp = br.readLine()) != null) { + //parse each line + splitted = tmp.split(";"); - //parse each line - splitted = tmp.split(";"); + //to determine the data index on the line. + int index = 0; - //to determine the data index on the line. - int index = 0; + //if there are row names, extract the first item as the row name + if (rowNames) { + this.rowNames.add(splitted[0]); + index = 1; + } - //if there are row names, extract the first item as the row name - if (rowNames) { - this.rowNames.add(splitted[0]); - index = 1; - } + for (int i = index; i < splitted.length; i++) { + //cast the data imported to the specified type. + //test the size of the inputType list. If 1 import all the + //columns as the type of the first element. - for (int i = index; i < splitted.length; i++) { - //cast the data imported to the specified type. - //test the size of the inputType list. If 1 import all the - //columns as the type of the first element. + //Get the column for index + ArrayList<Object> objects = (ArrayList<Object>)tempData.get(i - index); - //Get the column for index - ArrayList<Object> objects = (ArrayList<Object>)tempData.get(i - index); - - //add to the column the converted value. If importTypes contains - //only one element, cast into this type, else cast into the - //column type. - if (((importTypes.size() == 1) && + //add to the column the converted value. If importTypes contains + //only one element, cast into this type, else cast into the + //column type. + if (((importTypes.size() == 1) && (importTypes.get(0) instanceof String) ) || - ((importTypes.size() > (i -index )) && - (importTypes.get(i - index) instanceof String)) ) { + ((importTypes.size() > (i -index )) && + (importTypes.get(i - index) instanceof String)) ) { - //We import strings so no cast in case of string - objects.add(splitted[i]); + //We import strings so no cast in case of string + objects.add(splitted[i]); - } else if (((importTypes.size() == 1) && - (importTypes.get(0) instanceof Double) ) || - ((importTypes.size() > (i -index )) && - (importTypes.get(i - index) instanceof Double))) { + } else if (((importTypes.size() == 1) && + (importTypes.get(0) instanceof Double) ) || + ((importTypes.size() > (i -index )) && + (importTypes.get(i - index) instanceof Double))) { - //in case of Double - objects.add(Double.valueOf(splitted[i])); + //in case of Double + objects.add(Double.valueOf(splitted[i])); - } else if (((importTypes.size() == 1) && - (importTypes.get(0) instanceof Integer) ) || - ((importTypes.size() > (i -index )) && - (importTypes.get(i - index) instanceof Integer))) { + } else if (((importTypes.size() == 1) && + (importTypes.get(0) instanceof Integer) ) || + ((importTypes.size() > (i -index )) && + (importTypes.get(i - index) instanceof Integer))) { - //in case of Integer - objects.add(Integer.valueOf(splitted[i])); + //in case of Integer + objects.add(Integer.valueOf(splitted[i])); + } } } + } finally { + if (br != null){ + br.close(); + } } - br.close(); + this.data = tempData; if (log.isDebugEnabled()){ @@ -857,7 +883,13 @@ } - private void checkY(int y) { + /** + * Check if the index is into the data.frame length throws a + * IndexOutOfBoundsException if the index is too big. + * + * @param y index + */ + protected void checkY(int y) { if (!(this.data.get(0).isEmpty()) && (y > this.data.get(0).size())) { throw new IndexOutOfBoundsException(String.format(indexExceptionText, y, this.data.size())); @@ -866,7 +898,7 @@ /** * Check if the index is into the data.frame length throws a - * IndexOutOfBoundsException if not the index is too big. + * IndexOutOfBoundsException if the index is too big. * * @param x index */ @@ -878,7 +910,7 @@ } } - private void checkType(Object o) throws RException { + protected void checkType(Object o) throws RException { if (!(o instanceof String) && !(o instanceof Double) && !(o instanceof Integer) && !(o instanceof Boolean)) { throw new RException("Not supported type"); @@ -1001,12 +1033,13 @@ } } - String returnString = ""; + StringBuffer returnString = new StringBuffer(); for (String str:linesToDisplay){ - returnString+= str +"\n"; + returnString.append(str); + returnString.append("\n"); } - return returnString; + return returnString.toString(); } } Modified: trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-10-19 15:12:39 UTC (rev 240) +++ trunk/src/main/java/org/nuiton/j2r/types/REXPAbstract.java 2010-10-22 08:51:00 UTC (rev 241) @@ -352,12 +352,14 @@ this.names = names; //Create the r instruction (names(var)<-c("name 1",...,"name x")). - String namesString = ""; + StringBuilder namesString = new StringBuilder(""); for (int i = 0; i < this.names.size(); i++) { if (i != 0) { - namesString += ","; + namesString.append(","); } - namesString += "\"" + names.get(i) + "\""; + namesString.append("\""); + namesString.append(names.get(i)); + namesString.append("\""); } String rexp = String.format(RInstructions.SET_NAMES, this.variable, namesString); Modified: trunk/src/main/java/org/nuiton/j2r/types/RList.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-10-19 15:12:39 UTC (rev 240) +++ trunk/src/main/java/org/nuiton/j2r/types/RList.java 2010-10-22 08:51:00 UTC (rev 241) @@ -44,8 +44,8 @@ public class RList extends REXPAbstract implements REXP { //Content of the list (eg elements of the list in R) - private List<Object> data; - private Log log = LogFactory.getLog(RDataFrame.class); + protected List<Object> data; + protected Log log = LogFactory.getLog(RDataFrame.class); /** * Create a default RList linked to a R engine (the List is not initialized * in R.) @@ -138,20 +138,22 @@ @Override public String toRString() throws RException { checkVariable(); - String returnString = this.variable + "<-list("; + StringBuilder returnString = new StringBuilder(); + returnString.append(this.variable); + returnString.append("<-list("); if ((this.data != null) && (!(this.data.isEmpty()))) { for (int i = 0; i < data.size(); i++) { - returnString += toRString(i); + returnString.append(toRString(i)); } - returnString = returnString.substring(0, returnString.length() - 1); + returnString = new StringBuilder(returnString.substring(0, returnString.length() - 1)); } - returnString += ")"; + returnString.append(")"); if (log.isDebugEnabled()){ log.debug(returnString); } - return returnString; + return returnString.toString(); } /** @@ -160,7 +162,7 @@ * @return the corresponding R instruction * @throws RException if an error occur creating R instruction for REXPs */ - private String toRString(int i) throws RException { + protected String toRString(int i) throws RException { String returnString=""; Object obj = data.get(i); @@ -295,7 +297,7 @@ } - private void setInData(int x, Object data){ + protected void setInData(int x, Object data){ for (int i = 0; i <= x; i++) { try { this.data.get(i); @@ -431,20 +433,25 @@ @Override public String toString(){ - String returnString=""; + StringBuilder returnString = new StringBuilder(""); for(int i=0;i<this.data.size();i++){ //display the index if( (names!=null) && (!names.isEmpty()) && (names.get(i)!=null)){ - returnString += "[[" + names.get(i) + "]]\n"; + returnString.append("[["); + returnString.append(names.get(i)); + returnString.append("]]\n"); } else { - returnString += "[[" + i + "]]\n"; + returnString.append("[["); + returnString.append(i); + returnString.append("]]\n"); } //display the item at index i - returnString += this.data.get(i) + "\n\n"; + returnString.append(this.data.get(i)); + returnString.append("\n\n"); } - return returnString; + return returnString.toString(); } } Modified: trunk/src/site/rst/installTest.rst =================================================================== --- trunk/src/site/rst/installTest.rst 2010-10-19 15:12:39 UTC (rev 240) +++ trunk/src/site/rst/installTest.rst 2010-10-22 08:51:00 UTC (rev 241) @@ -1,3 +1,27 @@ +.. - +.. * #%L +.. * Nuiton Java-2-R library +.. * +.. * $Id$ +.. * $HeadURL$ +.. * %% +.. * Copyright (C) 2006 - 2010 CodeLutin +.. * %% +.. * This program is free software: you can redistribute it and/or modify +.. * it under the terms of the GNU Lesser General Public License as +.. * published by the Free Software Foundation, either version 3 of the +.. * License, or (at your option) any later version. +.. * +.. * This program is distributed in the hope that it will be useful, +.. * but WITHOUT ANY WARRANTY; without even the implied warranty of +.. * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +.. * GNU General Lesser Public License for more details. +.. * +.. * You should have received a copy of the GNU General Lesser Public +.. * License along with this program. If not, see +.. * <http://www.gnu.org/licenses/lgpl-3.0.html>. +.. * #L% +.. - Installer l'environnement de tests ================================== @@ -77,5 +101,12 @@ (C:\Program Files\R\R-(version) ou ...) (en fait sur le dossier contenant la librairie R.dll) +Lancer les tests +================ + +Il faut lancer un serveur Rserve, en lançant la commande :: + + R CMD Rserve + Tout doit maintenant être prêt et vous pouvez faire tourner les tests de nuiton-j2r. \ No newline at end of file Modified: trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java 2010-10-19 15:12:39 UTC (rev 240) +++ trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java 2010-10-22 08:51:00 UTC (rev 241) @@ -1,3 +1,27 @@ +/* + * #%L + * Nuiton Java-2-R library + * + * $Id$ + * $HeadURL$ + * %% + * Copyright (C) 2006 - 2010 CodeLutin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU Lesser General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Lesser Public License for more details. + * + * You should have received a copy of the GNU General Lesser Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/lgpl-3.0.html>. + * #L% + */ package org.nuiton.j2r; import java.io.File; Modified: trunk/src/test/java/org/nuiton/j2r/NetTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-10-19 15:12:39 UTC (rev 240) +++ trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-10-22 08:51:00 UTC (rev 241) @@ -8,16 +8,16 @@ * Copyright (C) 2006 - 2010 CodeLutin * %% * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU Lesser General Public License as - * published by the Free Software Foundation, either version 3 of the + * it under the terms of the GNU Lesser General Public License as + * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Lesser Public License for more details. - * - * You should have received a copy of the GNU General Lesser Public + * + * You should have received a copy of the GNU General Lesser Public * License along with this program. If not, see * <http://www.gnu.org/licenses/lgpl-3.0.html>. * #L%

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r240 - trunk/src/test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org Oct. 19, 2010

Oct. 19, 2010

Author: jcouteau Date: 2010-10-19 17:12:39 +0200 (Tue, 19 Oct 2010) New Revision: 240 Url: http://nuiton.org/repositories/revision/nuiton-j2r/240 Log: Add to test to prove anno #940 is obsolete Modified: trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java Modified: trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java 2010-10-19 14:47:28 UTC (rev 239) +++ trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java 2010-10-19 15:12:39 UTC (rev 240) @@ -382,4 +382,17 @@ Assert.assertTrue(pictureFile.exists()); //engine.eval("plot(seq(1,10))"); } + + @Test + public void testAno940RErrorNotThrown() throws Exception { + + try { + engine.eval("FiletPoisson-LangousteCorse(Langousterouge)" + + "(Selectivity).equation.Ktemp<-c(0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0,2.0)"); + Assert.fail("Exception should have been thrown"); + } catch (RException eee){ + Assert.assertTrue(eee.getMessage().contains("FiletPoisson-LangousteCorse(Langousterouge)(Selectivity).equation.Ktemp")); + } + + } }

1 0

r239 - trunk/src/license
by jcouteau＠users.nuiton.org Oct. 19, 2010

Oct. 19, 2010

Author: jcouteau Date: 2010-10-19 16:47:28 +0200 (Tue, 19 Oct 2010) New Revision: 239 Url: http://nuiton.org/repositories/revision/nuiton-j2r/239 Log: Add Third-party licenses Added: trunk/src/license/THIRD-PARTY.properties Added: trunk/src/license/THIRD-PARTY.properties =================================================================== --- trunk/src/license/THIRD-PARTY.properties (rev 0) +++ trunk/src/license/THIRD-PARTY.properties 2010-10-19 14:47:28 UTC (rev 239) @@ -0,0 +1,14 @@ +# Generated by org.nuiton.license.plugin.AddThirdPartyMojo +#------------------------------------------------------------------------------- +# Already used licenses in project : +# - BSD License +# - Common Public License Version 1.0 +# - The Apache Software License, Version 2.0 +#------------------------------------------------------------------------------- +# Please fill the missing licenses for dependencies : +# +# +#Mon Oct 18 12:45:36 CEST 2010 +org.nuiton.thirdparty--JRI--0.8-4=LGPLv2.1 +org.nuiton.thirdparty--REngine--0.6-1=LGPLv2.1 +org.nuiton.thirdparty--Rserve--0.6-1=LGPLv2.1

1 0

r238 - in trunk/src/site: . rst
by jcouteau＠users.nuiton.org Oct. 19, 2010

Oct. 19, 2010

Author: jcouteau Date: 2010-10-19 16:31:02 +0200 (Tue, 19 Oct 2010) New Revision: 238 Url: http://nuiton.org/repositories/revision/nuiton-j2r/238 Log: Add doc about how to install test environment Added: trunk/src/site/rst/installTest.rst Modified: trunk/src/site/site.xml Added: trunk/src/site/rst/installTest.rst =================================================================== --- trunk/src/site/rst/installTest.rst (rev 0) +++ trunk/src/site/rst/installTest.rst 2010-10-19 14:31:02 UTC (rev 238) @@ -0,0 +1,81 @@ +Installer l'environnement de tests +================================== + +Pour pouvoir effctuer les tests de nuiton-j2r, il faut un environnement +spécial : R doit être installé de même que Rserve, certaines variables +d'environnement doivent être déclarées et des librairies natives doivent être +utilisées. + +Installation de R +----------------- + +Pour installer R, référez-vous au site du projet : http://cran.r-project.org/ + +Pour information, sur les distributions linux de type debian/ubuntu, il faut +faire, en root, un petit :: + + apt-get install r-base-core + +Installation de Rserve +---------------------- + +Pour installer Rserve, deux solutions sont possibles. Soit démarrer R (sous +linux par la commande R) puis lancer la commande :: + + install.packages("Rserve") + +Soit, pour les utilisateurs linux, installer par les packets, soit pour +debian/ubuntu, en root :: + + apt-get install r-cran-rserve + +Installation de JRI +------------------- + +Pour installer JRI, le processus est plus complexe. Soit vous pouvez vous +satisfaire des versions précompilées, soit vous devrez compiler la librairie +pour votre système. + +Installation sans compilation +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Dans le dossier src/main/resources, vous pourrez trouver la librairie jri +précompilée pour la plupart des environnements. Vous pouvez la recompiler si +besoin, ou si les version précompilées ne fonctionnent pas. + +Copiez le fichier correspondant à votre système dans le dossier que vous +souhaitez. + +Passez maintenant à la phase de configuration + +Installation avec compilation +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Pour compiler la librairie, dézippez dans un premier temps l'archive +*JRI-sources.zip*. Ensuite, excécutez le script nommé "configure" de manière à +préparer votre système à la compilation. Enfin, effectuez la compilation à +l'aide de la commande "make". + +La compilation effectuée, un fichier a été généré, dont le nom est propre à la +plateforme (libjri.so, jri.dll, ...). + +Copiez le fichier correspondant à votre système dans le dossier que vous +souhaitez. + +Passez maintenant à la phase de configuration. + +Configuration +~~~~~~~~~~~~~ + +Vous devez modifier vos variables d'environnement : + +- R_HOME : doit pointer sur le dossier d'installation de R (soit /usr/lib/R sous + Linux ou C:\Program Files\R\R-(version) sous Windows ou ...) +- LD_LIBRARY_PATH : doit pointer sur le dossier lib contenu dans R_HOME (soit + R_HOME/lib/ sous Linux ou R_HOME\lib sous Windows ou ...) +- PATH (pour Windows) : doit pointer sur le dossier d'installation de R + (C:\Program Files\R\R-(version) ou ...) (en fait sur le dossier contenant la + librairie R.dll) + +Tout doit maintenant être prêt et vous pouvez faire tourner les tests de +nuiton-j2r. \ No newline at end of file Modified: trunk/src/site/site.xml =================================================================== --- trunk/src/site/site.xml 2010-10-19 14:28:46 UTC (rev 237) +++ trunk/src/site/site.xml 2010-10-19 14:31:02 UTC (rev 238) @@ -48,6 +48,7 @@ <item href="etude.html" name="Etude"/> <item href="installation.html" name="Installation"/> <item href="module.html" name="Utilisation"/> + <item href="installTest.html" name="Environnement de tests"/> </menu> <menu name="Téléchargement">

1 0

r237 - trunk/src/test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org Oct. 19, 2010

Oct. 19, 2010

Author: jcouteau Date: 2010-10-19 16:28:46 +0200 (Tue, 19 Oct 2010) New Revision: 237 Url: http://nuiton.org/repositories/revision/nuiton-j2r/237 Log: Use an abstract test to not duplicate common tests for R engines Added: trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java Modified: trunk/src/test/java/org/nuiton/j2r/JNITest.java trunk/src/test/java/org/nuiton/j2r/NetTest.java Added: trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java (rev 0) +++ trunk/src/test/java/org/nuiton/j2r/AbstractEngineTest.java 2010-10-19 14:28:46 UTC (rev 237) @@ -0,0 +1,385 @@ +package org.nuiton.j2r; + +import java.io.File; +import org.junit.Assert; +import org.junit.Test; +import org.nuiton.j2r.types.RDataFrame; +import org.nuiton.j2r.types.RList; + +import static org.nuiton.j2r.TestConstants.S_NB_LOOPS; +import static org.nuiton.j2r.TestConstants.S_OP; +import static org.nuiton.j2r.TestConstants.S_T_MAX; +import static org.nuiton.j2r.TestConstants.V_MAX; +import static org.nuiton.j2r.TestConstants.V_NB_LOOPS; +import static org.nuiton.j2r.TestConstants.V_OP_A; +import static org.nuiton.j2r.TestConstants.V_OP_AB; +import static org.nuiton.j2r.TestConstants.V_OP_B; +import static org.nuiton.j2r.TestConstants.V_OP_R; + +/** + * User: couteau + * Date: 19 oct. 2010 + */ +public abstract class AbstractEngineTest { + + protected REngine engine; + protected String savedRType; + + @Test + public void testDouble() throws Exception { + Assert.assertEquals(5.0, engine.eval("5.0")); + engine.voidEval("t<-sin(0)"); + double d = (Double) engine.eval("t"); + Assert.assertEquals(0.0, d, 0); + } + + @Test + public void testDoubleArray() throws Exception { + Object result = engine.eval("5.5:10.5"); + Assert.assertEquals(double[].class, result.getClass()); + double[] doubleArray = (double[]) result; + Assert.assertEquals(6, doubleArray.length); + for (int i = 5; i < 11; i++) { + double d = i + 0.5; + Assert.assertEquals(d, doubleArray[i - 5], 0); + } + } + + @Test + public void testSimpleOp() throws Exception { + LutinTimer t = new LutinTimer(); + for (int loop = 0; loop < S_NB_LOOPS; loop++) { + engine.voidEval("t<-0"); + t.startTiming(); + engine.voidEval(S_OP); + t.endTiming(); + double d = (Double) engine.eval("t"); + Assert.assertEquals((double) S_T_MAX, d, 0); + } + double[] results = t.computeResults(); + System.err.println("[SO]min: " + results[0]); + System.err.println("[SO]avg: " + results[1]); + System.err.println("[SO]max: " + results[2]); + System.err.println("[SO]etype: " + results[3]); + } + + @Test + public void testVector() throws Exception { + System.err.println(V_OP_R); + LutinTimer t = new LutinTimer(); + for (int loop = 0; loop < V_NB_LOOPS; loop++) { + t.startTiming(); + engine.voidEval(V_OP_A); + engine.voidEval(V_OP_B); + double[] r = (double[]) engine.eval(V_OP_AB); + t.endTiming(); + Assert.assertEquals(V_MAX, r.length); + } + double[] results = t.computeResults(); + System.err.println("[V]min: " + results[0]); + System.err.println("[V]avg: " + results[1]); + System.err.println("[V]max: " + results[2]); + System.err.println("[V]etype: " + results[3]); + } + + @Test + public void testString() throws Exception { + engine.voidEval("a<-\"testing string\""); + String testString = (String) engine.eval("a"); + Assert.assertEquals("testing string", testString); + } + + @Test + public void testInt() throws Exception { + engine.voidEval("a<-as.integer(5)"); + Integer testInteger = (Integer) engine.eval("a"); + Integer toCompare = 5; + Assert.assertEquals(toCompare, testInteger); + } + + @Test + public void testIntArray() throws Exception { + engine.voidEval("a<-as.integer(5)"); + engine.voidEval("b<-as.integer(6)"); + engine.voidEval("z<-c(a,b)"); + int[] testIntArray = (int[]) engine.eval("z"); + Assert.assertEquals(5, testIntArray[0]); + Assert.assertEquals(6, testIntArray[1]); + } + + @Test + public void testBool() throws Exception { + engine.voidEval("a<-TRUE"); + engine.voidEval("b<-FALSE"); + Boolean testA = (Boolean) engine.eval("a"); + Boolean testB = (Boolean) engine.eval("b"); + Assert.assertTrue(testA); + Assert.assertFalse(testB); + } + + @Test + public void testArrayBool() throws Exception { + engine.voidEval("a<-c(TRUE,FALSE,TRUE)"); + Boolean[] testBoolArray = (Boolean[]) engine.eval("a"); + Assert.assertTrue(testBoolArray[0]); + Assert.assertFalse(testBoolArray[1]); + Assert.assertTrue(testBoolArray[2]); + } + + @Test + public void testWorkingDirectory() throws Exception { + + //test linux paths + File workingDirectory = new File("/tmp"); + engine.setwd(workingDirectory); + File testWorkingDirectory = engine.getwd(); + Assert.assertEquals(workingDirectory.getAbsolutePath(), + testWorkingDirectory.getAbsolutePath()); + + //test windows paths + File tempFile = File.createTempFile("test", "", new File(System.getProperty("java.io.tmpdir"))); + Boolean tempBoolean = tempFile.delete(); + tempBoolean = tempFile.mkdirs(); + workingDirectory = new File(System.getProperty("java.io.tmpdir") + + "\\" + tempFile.getName()); + engine.setwd(workingDirectory); + testWorkingDirectory = engine.getwd(); + Assert.assertEquals(tempFile.getAbsolutePath(), + testWorkingDirectory.getAbsolutePath()); + } + + @Test + public void testRData() throws Exception { + File workingdir = new File("/tmp"); + engine.voidEval("a<-5.0"); + engine.saveRData(workingdir); + engine.remove("a"); + engine.loadRData(workingdir); + Double testDouble = (Double) engine.eval("a"); + Double compareTo = 5.0; + Assert.assertEquals(compareTo, testDouble); + } + + @Test + public void testDputDget() throws Exception { + File workingdir = new File("/tmp"); + File testingFile = new File("/tmp/testfile"); + + // test method using the workingdir + engine.voidEval("a<-5.0"); + engine.setwd(workingdir); + engine.dput("a", "testDputDgetfile"); + engine.remove("a"); + engine.dget("a", "testDputDgetfile"); + Double testDouble = (Double) engine.eval("a"); + Double compareTo = 5.0; + Assert.assertEquals(compareTo, testDouble); + + //test method using absolute path + workingdir = new File("/"); + engine.setwd(workingdir); + engine.voidEval("a<-6.0"); + engine.dput("a", testingFile); + engine.remove("a"); + engine.dget("a", testingFile); + Double testDouble2 = (Double) engine.eval("a"); + Double compareTo2 = 6.0; + Assert.assertEquals(compareTo2, testDouble2); + File testWorkingDirectory = engine.getwd(); + Assert.assertEquals(workingdir.getAbsolutePath(), + testWorkingDirectory.getAbsolutePath()); + } + + @Test + public void testRemove() throws Exception { + engine.voidEval("a<-6.0"); + Assert.assertEquals(6.0, engine.eval("a")); + try { + engine.remove("a"); + engine.eval("a"); + Assert.fail("Exception should have been thrown at this point"); + } catch (RException re) { + System.out.println(re.getMessage()); + Assert.assertTrue( + re.getMessage().contains("object \'a\' not found")); + } + } + + @Test + public void testMvCp() throws Exception { + //Test only mv as mv uses cp. + engine.voidEval("a<-5.0"); + engine.remove("b"); + engine.mv("a", "b"); + Assert.assertEquals(5.0, engine.eval("b")); + Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); + } + + @Test + public void testLsClearSession() throws Exception { + //Test only ClearSession as it uses ls + engine.voidEval("a<-5.0"); + engine.voidEval("b<-5.0"); + engine.voidEval("d<-5.0"); + engine.voidEval("e<-5.0"); + engine.voidEval("f<-5.0"); + engine.clearSession(); + Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"b\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"d\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"e\")")); + Assert.assertFalse((Boolean) engine.eval("exists(\"f\")")); + } + + @Test + public void testAutoCommitFalse() throws Exception { + engine.clearSession(); + engine.setAutoCommit(false); + engine.voidEval("a<-5.0"); + engine.voidEval("a<-a+5.0"); + engine.voidEval("b<-5.0"); + engine.voidEval("d<-5.0"); + engine.voidEval("e<-5.0"); + engine.voidEval("f<-5.0"); + engine.commit(); + Assert.assertEquals(10.0, engine.eval("a")); + Assert.assertEquals(5.0, engine.eval("b")); + Assert.assertEquals(5.0, engine.eval("d")); + Assert.assertEquals(5.0, engine.eval("e")); + Assert.assertEquals(5.0, engine.eval("f")); + } + + @Test + public void testThrowException() throws Exception { + engine.clearSession(); + //Test that the exception is normally thrown in voidEval + try { + engine.voidEval("a<-b"); + Assert.fail("Exception should have been thrown at this point"); + } catch (RException e) { + Assert.assertTrue( + e.getMessage().contains("object \'b\' not found")); + } + + engine.clearSession(); + //Test that the exception is normally thrown in eval + try { + engine.eval("a"); + Assert.fail("Exception should have been thrown at this point"); + } catch (RException e) { + Assert.assertTrue( + e.getMessage().contains("object \'a\' not found")); + } + } + + @Test + public void testDataFrame() throws Exception { + engine.voidEval("a<-data.frame(c(3,4,5,6),c(as.integer(3),as.integer(4),as.integer(5),as.integer(6)),c(\"a\",\"b\",\"c\",\"d\"),c(TRUE,FALSE,TRUE,FALSE),stringsAsFactors=FALSE)"); + RDataFrame testA = (RDataFrame) engine.eval("a"); + engine.setAutoCommit(false); + Assert.assertEquals(testA.get(0, 0), 3.0); + Assert.assertEquals(testA.get(0, 1), 4.0); + Assert.assertEquals(testA.get(0, 2), 5.0); + Assert.assertEquals(testA.get(0, 3), 6.0); + Assert.assertEquals(testA.get(1, 0), 3); + Assert.assertEquals(testA.get(1, 1), 4); + Assert.assertEquals(testA.get(1, 2), 5); + Assert.assertEquals(testA.get(1, 3), 6); + Assert.assertEquals(testA.get(2, 0), "a"); + Assert.assertEquals(testA.get(2, 1), "b"); + Assert.assertEquals(testA.get(2, 2), "c"); + Assert.assertEquals(testA.get(2, 3), "d"); + Assert.assertEquals(testA.get(3, 0), true); + Assert.assertEquals(testA.get(3, 1), false); + Assert.assertEquals(testA.get(3, 2), true); + Assert.assertEquals(testA.get(3, 3), false); + engine.setAutoCommit(true); + } + + @Test + public void testList() throws Exception { + //create a data.frame to be added to the list + engine.voidEval("b<-data.frame(c(3,4,5,6),c(as.integer(3),as.integer(4),as.integer(5),as.integer(6)),c(\"a\",\"b\",\"c\",\"d\"),c(TRUE,FALSE,TRUE,FALSE),stringsAsFactors=FALSE)"); + engine.voidEval("a<-list(one=as.integer(2),two=3.0,three=TRUE,four=\"b\",five=b)"); + RList testA = (RList) engine.eval("a"); + engine.setAutoCommit(false); + Assert.assertEquals(testA.get(0), 2); + Assert.assertEquals(testA.get(1), 3.0); + Assert.assertEquals(testA.get(2), true); + Assert.assertEquals(testA.get(3), "b"); + Assert.assertTrue(testA.get(4) instanceof RDataFrame); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(0, 0), 3.0); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(0, 1), 4.0); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(0, 2), 5.0); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(0, 3), 6.0); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(1, 0), 3); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(1, 1), 4); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(1, 2), 5); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(1, 3), 6); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(2, 0), "a"); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(2, 1), "b"); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(2, 2), "c"); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(2, 3), "d"); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(3, 0), true); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(3, 1), false); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(3, 2), true); + Assert.assertEquals(((RDataFrame) testA.get(4)).get(3, 3), false); + Assert.assertEquals(testA.getName(0), "one"); + Assert.assertEquals(testA.getName(1), "two"); + Assert.assertEquals(testA.getName(2), "three"); + Assert.assertEquals(testA.getName(3), "four"); + Assert.assertEquals(testA.getName(4), "five"); + engine.setAutoCommit(true); + + } + + @Test + public void testLongLines() throws Exception { + engine.voidEval("SensitivityBiomassY3<-c(2.179694924446179E7,2.179468496519559E7,2.1818736174725175E7,2.1816429067949396E7,2.1800098718126506E7,2.1838067907599747E7,2.183569971088971E7,2.1833313097146016E7,2.185719149559428E7,2.1854762634011697E7,2.185231549094628E7,2.187610838662306E7,2.187361928018277E7,2.1871112026349083E7,2.189482001091965E7,2.1892271074663457E7,2.1889704123663016E7,2.1913327781288046E7,2.1910719425357413E7,2.1908093185913157E7,2.193163309335182E7,2.192896572306039E7,2.1926280599087697E7,2.1949737325799696E7,2.1964830419511076E7,2.1944267732381735E7,2.1967641840627935E7,2.196485763859664E7,2.1962055938437656E7,2.198534798337946E7,2.198250595466467E7,2.19796465535838E7,2.2002857083381277E7,2.1999957614685252E7,2.1997040898068156E7,2.2020170453976974E7,2.2017213927520543E7,2.201424027629076E7,2.201424027629076E7,2.2007088929931033E7,2.1999922487316884E7,2.197681420767298E7,2.196962074430254E7,2.1962412278355762E7,2.1939244418647803E7,2.19320089340683E7,2.1924758538858987E7,2.1901530675850462E7,2.1894253260547817E7,2.1886961024817027E7,2.186367272884308E7,2.1856353467938498E7,2.1849019475049105E7,2.182567030993665E7,2.181830928313515E7,2.1810933611020483E7,2.1787523134007405E7,2.178012041554803E7,2.1772703136661157E7,2.1749230898314577E7,2.1749758710004635E7,2.1734327738178723E7,2.171079328231229E7,2.1703307381126277E7,2.1695807083871227E7,2.167220994746149E7,2.1664682544012114E7,2.1657140823937435E7,2.1633480537039224E7,2.162591168317374E7,2.161832859028344E7,2.1594604675944276E7,2.158699441777762E7,2.157936999632849E7,2.1555581970502105E7,2.1547930348361045E7,2.155103621183836E7,2.152717169457966E7,2.1530236120902758E7,2.153328412702021E7,2.1509330625330385E7,2.1512336892940816E7,2.1515326604867205E7,2.1491283471099153E7,2.1494231139260102E7,2.1497162114652816E7,2.147302869279387E7,2.14759173151992E7,2.147878910612182E7,2.1454564731677204E7,2.1457393856367446E7,2.1462383791402113E7,2.1435890009080574E7,2.143865917835912E7,2.1441411233736E7,2.1417002926115625E7,2.141971167646219E7,2.1424717356960263E7,2.1397901863381278E7,2.1400549725365438E7,2.140318018420746E7,2.137858518066629E7,2.1381171678860184E7,2.1383740626669012E7,2.135905121665088E7,2.1361575869539354E7,2.1364082823016256E7,2.1339298288600616E7,2.1341760608492017E7,2.1344205078135047E7,2.1319324692060333E7,2.1321724184994433E7,2.132410567500613E7,2.132410567500613E7,2.1331536055398986E7,2.133895052044593E7,2.1363853672607094E7,2.137123650604985E7,2.137860336066902E7,2.140343328441597E7,2.1410768581059605E7,2.1418087833224125E7,2.1442845113907605E7,2.1450132877092432E7,2.1457404527983494E7,2.148208974251862E7,2.1489329968841057E7,2.1496554012913797E7,2.1521167729882605E7,2.1528360409261446E7,2.1535536834311184E7,2.1560079614063937E7,2.156722472980476E7,2.1563254271749333E7,2.1598825911786724E7,2.1605923440646578E7,2.1613004564718306E7,2.1637407118662428E7,2.1644457030912723E7,2.1651490460029803E7,2.167582370941422E7,2.1682825968903817E7,2.1689811664860353E7,2.171407613809878E7,2.1721030702315085E7,2.172796862056064E7,2.1752164838324733E7,2.1759071658455327E7,2.1765961748155564E7,2.1790090223469418E7,2.179694924446179E7,2.180379144855871E7,2.182785268689249E7,2.18346638475134E7,2.184145810278461E7,2.1865452602147E7,2.1872215835041337E7,2.1878962072157502E7,2.1902890323187094E7,2.1909605554935444E7,2.191630369851899E7,2.1940166184574656E7,2.1946833335751027E7,2.1953483304432537E7,2.1977280501682773E7,2.198389948690986E7,2.1990501193384256E7,2.20142335708955E7,2.2020804298901647E7,2.20273576499835E7,2.205102566980741E7,2.205754804348026E7,2.2064052940158665E7,2.20876570574184E7,2.2094130973859813E7,2.2100587311352342E7,2.2124127974327955E7,2.2130553324907117E7,2.2136960992712937E7,2.2160438642925616E7,2.2166815313332282E7,2.2173174195284456E7,2.2196589267580014E7,2.2202917137875687E7,2.2209227112193614E7,2.2232580034824714E7,2.2238858979494706E7,2.2245119918834776E7,2.2245119918834776E7,2.2247156092664756E7,2.2249172537482113E7,2.222580215006561E7,2.2227776978241052E7,2.2229731947289977E7,2.2206281851083208E7,2.2208194947734725E7,2.221008805387345E7,2.2186557726205546E7,2.2188408701148424E7,2.219023955290159E7,2.2166628464420535E7,2.2168416923091725E7,2.217018512458671E7,2.2146492739166215E7,2.2148218282559495E7,2.214992343346224E7,2.2126149208107647E7,2.212781143270992E7,2.21294531281596E7,2.21055965129125E7,2.21071950106372E7,2.21087728411807E7,2.2084833279022325E7,2.208636763714323E7,2.2087881188668158E7,2.2063858115421828E7,2.2065327916506168E7,2.2066776770173687E7,2.2042669614405714E7,2.2044074436245814E7,2.2045458168422367E7,2.2021266351342022E7,2.2022605766886715E7,2.2023923949074898E7,2.1999646884433046E7,2.200092046171817E7,2.1995009663381506E7,2.1970654681075428E7,2.196470853722463E7,2.195874261494959E7,2.1934317104578134E7,2.1928315823420756E7,2.1922294864394967E7,2.1897798306555357E7,2.1891741970889103E7,2.1885666055779688E7,2.1861097923225783E7,2.1854986609282427E7,2.1848855812173687E7,2.1824215569718488E7,2.18180493471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+ double[] test = (double[]) engine.eval("SensitivityBiomassY3"); + Assert.assertEquals(1500, test.length); + } + + @Test + public void testNonRegretionOnErrorFromR() throws Exception { + try { + engine.voidEval("dfresults<-data.frame(c(1,2,3),c(4,5,6))"); + } catch (NullPointerException npe) { + Assert.fail("Error should not have been thrown : " + npe); + } + } + + @Test + public void testListWithNullNames() throws Exception { + RList b = new RList(engine); + try { + b = (RList) engine.eval("b<-list(\"a\",\"b\")"); + b.setVariable("b"); + } catch (NullPointerException npe) { + npe.printStackTrace(); + Assert.fail("Error should not have been thrown : " + npe); + } + + Assert.assertEquals("a", b.get(0)); + Assert.assertEquals("b", b.get(1)); + + } + + @Test + public void testScripts() throws Exception { + double d = (Double) engine.evalScript("t<-sin(0)\nt"); + Assert.assertEquals(0.0, d, 0.001); + } + + @Test + public void testGraphics() throws Exception { + + File workingDirectory = new File("/tmp"); + engine.setwd(workingDirectory); + + engine.plot("test", "seq(1,10)", null, null, null, null, null, null, null); + File pictureFile = new File("/tmp/test.jpg"); + Assert.assertTrue(pictureFile.exists()); + //engine.eval("plot(seq(1,10))"); + } +} Modified: trunk/src/test/java/org/nuiton/j2r/JNITest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-10-18 09:43:32 UTC (rev 236) +++ trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-10-19 14:28:46 UTC (rev 237) @@ -38,24 +38,14 @@ import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.junit.After; -import org.junit.Assert; import org.junit.Assume; import org.junit.Before; import org.junit.BeforeClass; -import org.junit.Test; import org.nuiton.j2r.jni.RJniEngine; -import org.nuiton.j2r.types.RDataFrame; -import org.nuiton.j2r.types.RList; -import java.io.File; +public class JNITest extends AbstractEngineTest { -import static org.nuiton.j2r.TestConstants.*; - -public class JNITest { - private static Log log = LogFactory.getLog(JNITest.class); - private REngine engine; - private String savedRType; @BeforeClass public static void tryREnv() { @@ -115,364 +105,5 @@ } System.setProperty("R.type", savedRType); } - - @Test - public void testDouble() throws Exception { - Assert.assertEquals(5.0, engine.eval("5.0")); - engine.voidEval("t<-sin(0)"); - double d = (Double) engine.eval("t"); - Assert.assertEquals(0.0, d, 0); - } - - @Test - public void testDoubleArray() throws Exception { - Object result = engine.eval("5.5:10.5"); - Assert.assertEquals(double[].class, result.getClass()); - double[] doubleArray = (double[]) result; - Assert.assertEquals(6, doubleArray.length); - for (int i = 5; i < 11; i++) { - double d = i + 0.5; - Assert.assertEquals(d, doubleArray[i - 5], 0); - } - } - - @Test - public void testSimpleOp() throws Exception { - LutinTimer t = new LutinTimer(); - for (int loop = 0; loop < S_NB_LOOPS; loop++) { - engine.voidEval("t<-0"); - t.startTiming(); - engine.voidEval(S_OP); - t.endTiming(); - double d = (Double) engine.eval("t"); - Assert.assertEquals((double) S_T_MAX, d, 0); - } - double[] results = t.computeResults(); - System.err.println("[SO]min: " + results[0]); - System.err.println("[SO]avg: " + results[1]); - System.err.println("[SO]max: " + results[2]); - System.err.println("[SO]etype: " + results[3]); - } - - @Test - public void testVector() throws Exception { - System.err.println(V_OP_R); - LutinTimer t = new LutinTimer(); - for (int loop = 0; loop < V_NB_LOOPS; loop++) { - t.startTiming(); - engine.voidEval(V_OP_A); - engine.voidEval(V_OP_B); - double[] r = (double[]) engine.eval(V_OP_AB); - t.endTiming(); - Assert.assertEquals(V_MAX, r.length); - } - double[] results = t.computeResults(); - System.err.println("[V]min: " + results[0]); - System.err.println("[V]avg: " + results[1]); - System.err.println("[V]max: " + results[2]); - System.err.println("[V]etype: " + results[3]); - } - - @Test - public void testString() throws Exception { - engine.voidEval("a<-\"testing string\""); - String testString = (String) engine.eval("a"); - Assert.assertEquals("testing string", testString); - } - - @Test - public void testInt() throws Exception { - engine.voidEval("a<-as.integer(5)"); - Integer testInteger = (Integer) engine.eval("a"); - Integer toCompare = 5; - Assert.assertEquals(toCompare, testInteger); - } - - @Test - public void testIntArray() throws Exception { - engine.voidEval("a<-as.integer(5)"); - engine.voidEval("b<-as.integer(6)"); - engine.voidEval("z<-c(a,b)"); - int[] testIntArray = (int[]) engine.eval("z"); - Assert.assertEquals(5, testIntArray[0]); - Assert.assertEquals(6, testIntArray[1]); - } - - @Test - public void testBool() throws Exception { - engine.voidEval("a<-TRUE"); - engine.voidEval("b<-FALSE"); - Boolean testA = (Boolean) engine.eval("a"); - Boolean testB = (Boolean) engine.eval("b"); - Assert.assertTrue(testA); - Assert.assertFalse(testB); - } - - @Test - public void testArrayBool() throws Exception { - engine.voidEval("a<-c(TRUE,FALSE,TRUE)"); - Boolean[] testBoolArray = (Boolean[]) engine.eval("a"); - Assert.assertTrue(testBoolArray[0]); - Assert.assertFalse(testBoolArray[1]); - Assert.assertTrue(testBoolArray[2]); - } - - @Test - public void testWorkingDirectory() throws Exception { - - //test linux paths - File workingDirectory = new File("/tmp"); - engine.setwd(workingDirectory); - File testWorkingDirectory = engine.getwd(); - Assert.assertEquals(workingDirectory.getAbsolutePath(), - testWorkingDirectory.getAbsolutePath()); - - //test windows paths - File tempFile = File.createTempFile("test","", new File(System.getProperty("java.io.tmpdir"))); - Boolean tempBoolean = tempFile.delete(); - tempBoolean = tempFile.mkdirs(); - workingDirectory = new File(System.getProperty("java.io.tmpdir") + - "\\" + tempFile.getName()); - engine.setwd(workingDirectory); - testWorkingDirectory = engine.getwd(); - Assert.assertEquals(tempFile.getAbsolutePath(), - testWorkingDirectory.getAbsolutePath()); - } - - @Test - public void testRData() throws Exception { - File workingdir = new File("/tmp"); - engine.voidEval("a<-5.0"); - engine.saveRData(workingdir); - engine.remove("a"); - engine.loadRData(workingdir); - Double testDouble = (Double) engine.eval("a"); - Double compareTo = 5.0; - Assert.assertEquals(compareTo, testDouble); - } - - @Test - public void testDputDget() throws Exception { - File workingdir = new File("/tmp"); - File testingFile = new File("/tmp/testfile"); - - // test method using the workingdir - engine.voidEval("a<-5.0"); - engine.setwd(workingdir); - engine.dput("a", "testDputDgetfile"); - engine.remove("a"); - engine.dget("a", "testDputDgetfile"); - Double testDouble = (Double) engine.eval("a"); - Double compareTo = 5.0; - Assert.assertEquals(compareTo, testDouble); - - //test method using absolute path - workingdir = new File("/"); - engine.setwd(workingdir); - engine.voidEval("a<-6.0"); - engine.dput("a", testingFile); - engine.remove("a"); - engine.dget("a", testingFile); - Double testDouble2 = (Double) engine.eval("a"); - Double compareTo2 = 6.0; - Assert.assertEquals(compareTo2, testDouble2); - File testWorkingDirectory = engine.getwd(); - Assert.assertEquals(workingdir.getAbsolutePath(), - testWorkingDirectory.getAbsolutePath()); - } - - @Test - public void testRemove() throws Exception { - engine.voidEval("a<-6.0"); - Assert.assertEquals(6.0, engine.eval("a")); - try { - engine.remove("a"); - engine.eval("a"); - Assert.fail("Exception should have been thrown at this point"); - } catch (RException re) { - System.out.println(re.getMessage()); - Assert.assertTrue( - re.getMessage().contains("object \'a\' not found")); - } - } - - @Test - public void testMvCp() throws Exception { - //Test only mv as mv uses cp. - engine.voidEval("a<-5.0"); - engine.remove("b"); - engine.mv("a", "b"); - Assert.assertEquals(5.0, engine.eval("b")); - Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); - } - - @Test - public void testLsClearSession() throws Exception { - //Test only ClearSession as it uses ls - engine.voidEval("a<-5.0"); - engine.voidEval("b<-5.0"); - engine.voidEval("d<-5.0"); - engine.voidEval("e<-5.0"); - engine.voidEval("f<-5.0"); - engine.clearSession(); - Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); - Assert.assertFalse((Boolean) engine.eval("exists(\"b\")")); - Assert.assertFalse((Boolean) engine.eval("exists(\"d\")")); - Assert.assertFalse((Boolean) engine.eval("exists(\"e\")")); - Assert.assertFalse((Boolean) engine.eval("exists(\"f\")")); - } - - @Test - public void testAutoCommitFalse() throws Exception { - engine.clearSession(); - engine.setAutoCommit(false); - engine.voidEval("a<-5.0"); - engine.voidEval("a<-a+5.0"); - engine.voidEval("b<-5.0"); - engine.voidEval("d<-5.0"); - engine.voidEval("e<-5.0"); - engine.voidEval("f<-5.0"); - engine.commit(); - Assert.assertEquals(10.0, engine.eval("a")); - Assert.assertEquals(5.0, engine.eval("b")); - Assert.assertEquals(5.0, engine.eval("d")); - Assert.assertEquals(5.0, engine.eval("e")); - Assert.assertEquals(5.0, engine.eval("f")); - } - - @Test - public void testThrowException() throws Exception { - engine.clearSession(); - //Test that the exception is normally thrown in voidEval - try { - engine.voidEval("a<-b"); - Assert.fail("Exception should have been thrown at this point"); - } catch (RException e) { - log.info(e.getMessage()); - Assert.assertTrue( - e.getMessage().contains("object \'b\' not found")); - } - - engine.clearSession(); - //Test that the exception is normally thrown in eval - try { - engine.eval("a"); - Assert.fail("Exception should have been thrown at this point"); - } catch (RException e) { - Assert.assertTrue( - e.getMessage().contains("object \'a\' not found")); - } - } - - @Test - public void testDataFrame() throws Exception { - engine.voidEval("a<-data.frame(c(3,4,5,6),c(as.integer(3),as.integer(4),as.integer(5),as.integer(6)),c(\"a\",\"b\",\"c\",\"d\"),c(TRUE,FALSE,TRUE,FALSE),stringsAsFactors=FALSE)"); - RDataFrame testA = (RDataFrame) engine.eval("a"); - engine.setAutoCommit(false); - Assert.assertEquals(testA.get(0,0),3.0); - Assert.assertEquals(testA.get(0,1),4.0); - Assert.assertEquals(testA.get(0,2),5.0); - Assert.assertEquals(testA.get(0,3),6.0); - Assert.assertEquals(testA.get(1,0),3); - Assert.assertEquals(testA.get(1,1),4); - Assert.assertEquals(testA.get(1,2),5); - Assert.assertEquals(testA.get(1,3),6); - Assert.assertEquals(testA.get(2,0),"a"); - Assert.assertEquals(testA.get(2,1),"b"); - Assert.assertEquals(testA.get(2,2),"c"); - Assert.assertEquals(testA.get(2,3),"d"); - Assert.assertEquals(testA.get(3,0),true); - Assert.assertEquals(testA.get(3,1),false); - Assert.assertEquals(testA.get(3,2),true); - Assert.assertEquals(testA.get(3,3),false); - engine.setAutoCommit(true); - } - - @Test - public void testList() throws Exception { - //create a data.frame to be added to the list - engine.voidEval("b<-data.frame(c(3,4,5,6),c(as.integer(3),as.integer(4),as.integer(5),as.integer(6)),c(\"a\",\"b\",\"c\",\"d\"),c(TRUE,FALSE,TRUE,FALSE),stringsAsFactors=FALSE)"); - engine.voidEval("a<-list(one=as.integer(2),two=3.0,three=TRUE,four=\"b\",five=b)"); - RList testA = (RList)engine.eval("a"); - engine.setAutoCommit(false); - Assert.assertEquals(testA.get(0), 2); - Assert.assertEquals(testA.get(1), 3.0); - Assert.assertEquals(testA.get(2), true); - Assert.assertEquals(testA.get(3), "b"); - Assert.assertTrue(testA.get(4) instanceof RDataFrame); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(0,0), 3.0); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(0,1), 4.0); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(0,2), 5.0); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(0,3), 6.0); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(1,0), 3); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(1,1), 4); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(1,2), 5); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(1,3), 6); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(2,0), "a"); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(2,1), "b"); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(2,2), "c"); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(2,3), "d"); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(3,0), true); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(3,1), false); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(3,2), true); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(3,3), false); - Assert.assertEquals(testA.getName(0),"one"); - Assert.assertEquals(testA.getName(1),"two"); - Assert.assertEquals(testA.getName(2),"three"); - Assert.assertEquals(testA.getName(3),"four"); - Assert.assertEquals(testA.getName(4),"five"); - engine.setAutoCommit(true); - - } - - @Test - public void testLongLines() throws Exception{ - engine.voidEval("SensitivityBiomassY3<-c(2.179694924446179E7,2.179468496519559E7,2.1818736174725175E7,2.1816429067949396E7,2.1800098718126506E7,2.1838067907599747E7,2.183569971088971E7,2.1833313097146016E7,2.185719149559428E7,2.1854762634011697E7,2.185231549094628E7,2.187610838662306E7,2.187361928018277E7,2.1871112026349083E7,2.189482001091965E7,2.1892271074663457E7,2.1889704123663016E7,2.1913327781288046E7,2.1910719425357413E7,2.1908093185913157E7,2.193163309335182E7,2.192896572306039E7,2.1926280599087697E7,2.1949737325799696E7,2.1964830419511076E7,2.1944267732381735E7,2.1967641840627935E7,2.196485763859664E7,2.1962055938437656E7,2.198534798337946E7,2.198250595466467E7,2.19796465535838E7,2.2002857083381277E7,2.1999957614685252E7,2.1997040898068156E7,2.2020170453976974E7,2.2017213927520543E7,2.201424027629076E7,2.201424027629076E7,2.2007088929931033E7,2.1999922487316884E7,2.197681420767298E7,2.196962074430254E7,2.1962412278355762E7,2.1939244418647803E7,2.19320089340683E7,2.1924758538858987E7,2.1901530675850462E7,2.1894253260547817E7,2.1886961024817027E7,2.186367272884308E7,2.1856353467938498E7,2.1849019475049105E7,2.182567030993665E7,2.181830928313515E7,2.1810933611020483E7,2.1787523134007405E7,2.178012041554803E7,2.1772703136661157E7,2.1749230898314577E7,2.1749758710004635E7,2.1734327738178723E7,2.171079328231229E7,2.1703307381126277E7,2.1695807083871227E7,2.167220994746149E7,2.1664682544012114E7,2.1657140823937435E7,2.1633480537039224E7,2.162591168317374E7,2.161832859028344E7,2.1594604675944276E7,2.158699441777762E7,2.157936999632849E7,2.1555581970502105E7,2.1547930348361045E7,2.155103621183836E7,2.152717169457966E7,2.1530236120902758E7,2.153328412702021E7,2.1509330625330385E7,2.1512336892940816E7,2.1515326604867205E7,2.1491283471099153E7,2.1494231139260102E7,2.1497162114652816E7,2.147302869279387E7,2.14759173151992E7,2.147878910612182E7,2.1454564731677204E7,2.1457393856367446E7,2.1462383791402113E7,2.1435890009080574E7,2.143865917835912E7,2.1441411233736E7,2.1417002926115625E7,2.141971167646219E7,2.1424717356960263E7,2.1397901863381278E7,2.1400549725365438E7,2.140318018420746E7,2.137858518066629E7,2.1381171678860184E7,2.1383740626669012E7,2.135905121665088E7,2.1361575869539354E7,2.1364082823016256E7,2.1339298288600616E7,2.1341760608492017E7,2.1344205078135047E7,2.1319324692060333E7,2.1321724184994433E7,2.132410567500613E7,2.132410567500613E7,2.1331536055398986E7,2.133895052044593E7,2.1363853672607094E7,2.137123650604985E7,2.137860336066902E7,2.140343328441597E7,2.1410768581059605E7,2.1418087833224125E7,2.1442845113907605E7,2.1450132877092432E7,2.1457404527983494E7,2.148208974251862E7,2.1489329968841057E7,2.1496554012913797E7,2.1521167729882605E7,2.1528360409261446E7,2.1535536834311184E7,2.1560079614063937E7,2.156722472980476E7,2.1563254271749333E7,2.1598825911786724E7,2.1605923440646578E7,2.1613004564718306E7,2.1637407118662428E7,2.1644457030912723E7,2.1651490460029803E7,2.167582370941422E7,2.1682825968903817E7,2.1689811664860353E7,2.171407613809878E7,2.1721030702315085E7,2.172796862056064E7,2.1752164838324733E7,2.1759071658455327E7,2.1765961748155564E7,2.1790090223469418E7,2.179694924446179E7,2.180379144855871E7,2.182785268689249E7,2.18346638475134E7,2.184145810278461E7,2.1865452602147E7,2.1872215835041337E7,2.1878962072157502E7,2.1902890323187094E7,2.1909605554935444E7,2.191630369851899E7,2.1940166184574656E7,2.1946833335751027E7,2.1953483304432537E7,2.1977280501682773E7,2.198389948690986E7,2.1990501193384256E7,2.20142335708955E7,2.2020804298901647E7,2.20273576499835E7,2.205102566980741E7,2.205754804348026E7,2.2064052940158665E7,2.20876570574184E7,2.2094130973859813E7,2.2100587311352342E7,2.2124127974327955E7,2.2130553324907117E7,2.2136960992712937E7,2.2160438642925616E7,2.2166815313332282E7,2.2173174195284456E7,2.2196589267580014E7,2.2202917137875687E7,2.2209227112193614E7,2.2232580034824714E7,2.2238858979494706E7,2.2245119918834776E7,2.2245119918834776E7,2.2247156092664756E7,2.2249172537482113E7,2.222580215006561E7,2.2227776978241052E7,2.2229731947289977E7,2.2206281851083208E7,2.2208194947734725E7,2.221008805387345E7,2.2186557726205546E7,2.2188408701148424E7,2.219023955290159E7,2.2166628464420535E7,2.2168416923091725E7,2.217018512458671E7,2.2146492739166215E7,2.2148218282559495E7,2.214992343346224E7,2.2126149208107647E7,2.212781143270992E7,2.21294531281596E7,2.21055965129125E7,2.21071950106372E7,2.21087728411807E7,2.2084833279022325E7,2.208636763714323E7,2.2087881188668158E7,2.2063858115421828E7,2.2065327916506168E7,2.2066776770173687E7,2.2042669614405714E7,2.2044074436245814E7,2.2045458168422367E7,2.2021266351342022E7,2.2022605766886715E7,2.2023923949074898E7,2.1999646884433046E7,2.200092046171817E7,2.1995009663381506E7,2.1970654681075428E7,2.196470853722463E7,2.195874261494959E7,2.1934317104578134E7,2.1928315823420756E7,2.1922294864394967E7,2.1897798306555357E7,2.1891741970889103E7,2.1885666055779688E7,2.1861097923225783E7,2.1854986609282427E7,2.1848855812173687E7,2.1824215569718488E7,2.18180493471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- double[] test = (double[])engine.eval("SensitivityBiomassY3"); - Assert.assertEquals(1500, test.length); - } - - @Test - public void testNonRegretionOnErrorFromR() throws Exception{ - try{ - engine.voidEval("dfresults<-data.frame(c(1,2,3),c(4,5,6))"); - } catch (NullPointerException npe){ - Assert.fail("Error should not have been thrown : " + npe); - } - } - - @Test - public void testListWithNullNames() throws Exception { - RList b= new RList(engine); - try { - b = (RList)engine.eval("b<-list(\"a\",\"b\")"); - b.setVariable("b"); - } catch (NullPointerException npe) { - npe.printStackTrace(); - Assert.fail("Error should not have been thrown : " + npe); - } - - Assert.assertEquals("a",b.get(0)); - Assert.assertEquals("b", b.get(1)); - - } - - @Test - public void testScripts() throws Exception { - double d = (Double)engine.evalScript("t<-sin(0)\nt"); - Assert.assertEquals(0.0,d,0.001); - } - - @Test - public void testGraphics() throws Exception { - - File workingDirectory = new File("/tmp"); - engine.setwd(workingDirectory); - - engine.plot("test","seq(1,10)",null,null,null,null,null,null,null); - File pictureFile = new File("/tmp/test.jpg"); - Assert.assertTrue(pictureFile.exists()); - //engine.eval("plot(seq(1,10))"); - } } // JNITest Modified: trunk/src/test/java/org/nuiton/j2r/NetTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-10-18 09:43:32 UTC (rev 236) +++ trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-10-19 14:28:46 UTC (rev 237) @@ -35,29 +35,15 @@ * par : */ package org.nuiton.j2r; -import static org.nuiton.j2r.TestConstants.S_NB_LOOPS; -import static org.nuiton.j2r.TestConstants.S_OP; -import static org.nuiton.j2r.TestConstants.S_T_MAX; -import static org.nuiton.j2r.TestConstants.V_MAX; -import static org.nuiton.j2r.TestConstants.V_NB_LOOPS; -import static org.nuiton.j2r.TestConstants.V_OP_A; -import static org.nuiton.j2r.TestConstants.V_OP_AB; -import static org.nuiton.j2r.TestConstants.V_OP_B; -import java.io.File; - import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.junit.After; -import org.junit.Assert; import org.junit.Assume; import org.junit.Before; import org.junit.BeforeClass; -import org.junit.Test; import org.nuiton.j2r.net.RNetEngine; -import org.nuiton.j2r.types.RDataFrame; -import org.nuiton.j2r.types.RList; -public class NetTest { +public class NetTest extends AbstractEngineTest { private static Log log = LogFactory.getLog(NetTest.class); private REngine engine; @@ -121,318 +107,5 @@ System.setProperty("R.type", savedRType); } - @Test - public void testDouble() throws Exception { - Assert.assertEquals(5.0, engine.eval("5.0")); - engine.voidEval("t<-sin(0)"); - double d = (Double) engine.eval("t"); - Assert.assertEquals(0.0, d, 0); - } - @Test - public void testIntArray() throws Exception { - Object result = engine.eval("5:10"); - Assert.assertNotNull(result); - Assert.assertEquals(int[].class, result.getClass()); - int[] intArray = (int[]) result; - Assert.assertEquals(6, intArray.length); - for (int i = 5; i < 11; i++) { - Assert.assertEquals(i, intArray[i - 5]); - } - } - - @Test - public void testSimpleOp() throws Exception { - LutinTimer t = new LutinTimer(); - for (int loop = 0; loop < S_NB_LOOPS; loop++) { - engine.voidEval("t<-0"); - t.startTiming(); - engine.voidEval(S_OP); - t.endTiming(); - double d = (Double) engine.eval("t"); - Assert.assertEquals((double) S_T_MAX, d, 0); - } - double[] results = t.computeResults(); - System.err.println("[SO]min: " + results[0]); - System.err.println("[SO]avg: " + results[1]); - System.err.println("[SO]max: " + results[2]); - System.err.println("[SO]etype: " + results[3]); - } - - @Test - public void testVector() throws Exception { - LutinTimer t = new LutinTimer(); - for (int loop = 0; loop < V_NB_LOOPS; loop++) { - t.startTiming(); - engine.voidEval(V_OP_A); - engine.voidEval(V_OP_B); - double[] r = (double[]) engine.eval(V_OP_AB); - t.endTiming(); - Assert.assertEquals(V_MAX, r.length); - } - double[] results = t.computeResults(); - System.err.println("[V]min: " + results[0]); - System.err.println("[V]avg: " + results[1]); - System.err.println("[V]max: " + results[2]); - System.err.println("[V]etype: " + results[3]); - } - - @Test - public void testString() throws Exception { - engine.voidEval("a<-\"testing string\""); - String testString = (String) engine.eval("a"); - Assert.assertEquals("testing string", testString); - } - - @Test - public void testInt() throws Exception { - engine.voidEval("a<-as.integer(5)"); - Integer testInteger = (Integer) engine.eval("a"); - Integer toCompare = 5; - Assert.assertEquals(toCompare, testInteger); - } - - @Test - public void testBool() throws Exception { - engine.voidEval("a<-TRUE"); - engine.voidEval("b<-FALSE"); - Boolean testA = (Boolean) engine.eval("a"); - Boolean testB = (Boolean) engine.eval("b"); - Assert.assertTrue(testA); - Assert.assertFalse(testB); - } - - @Test - public void testDataFrame() throws Exception { - engine.voidEval("a<-data.frame(c(3,4,5,6),c(as.integer(3),as.integer(4),as.integer(5),as.integer(6)),c(\"a\",\"b\",\"c\",\"d\"),c(TRUE,FALSE,TRUE,FALSE),stringsAsFactors=FALSE)"); - RDataFrame testA = (RDataFrame) engine.eval("a"); - engine.setAutoCommit(false); - Assert.assertEquals(testA.get(0,0),3.0); - Assert.assertEquals(testA.get(0,1),4.0); - Assert.assertEquals(testA.get(0,2),5.0); - Assert.assertEquals(testA.get(0,3),6.0); - Assert.assertEquals(testA.get(1,0),3); - Assert.assertEquals(testA.get(1,1),4); - Assert.assertEquals(testA.get(1,2),5); - Assert.assertEquals(testA.get(1,3),6); - Assert.assertEquals(testA.get(2,0),"a"); - Assert.assertEquals(testA.get(2,1),"b"); - Assert.assertEquals(testA.get(2,2),"c"); - Assert.assertEquals(testA.get(2,3),"d"); - Assert.assertEquals(testA.get(3,0),true); - Assert.assertEquals(testA.get(3,1),false); - Assert.assertEquals(testA.get(3,2),true); - Assert.assertEquals(testA.get(3,3),false); - engine.setAutoCommit(true); - } - - @Test - public void testList() throws Exception { - //create a data.frame to be added to the list - engine.voidEval("b<-data.frame(c(3,4,5,6),c(as.integer(3),as.integer(4),as.integer(5),as.integer(6)),c(\"a\",\"b\",\"c\",\"d\"),c(TRUE,FALSE,TRUE,FALSE),stringsAsFactors=FALSE)"); - engine.voidEval("a<-list(one=as.integer(2),two=3.0,three=TRUE,four=\"b\",five=b)"); - RList testA = (RList)engine.eval("a"); - engine.setAutoCommit(false); - Assert.assertEquals(testA.get(0), 2); - Assert.assertEquals(testA.get(1), 3.0); - Assert.assertEquals(testA.get(2), true); - Assert.assertEquals(testA.get(3), "b"); - Assert.assertTrue(testA.get(4) instanceof RDataFrame); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(0,0), 3.0); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(0,1), 4.0); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(0,2), 5.0); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(0,3), 6.0); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(1,0), 3); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(1,1), 4); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(1,2), 5); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(1,3), 6); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(2,0), "a"); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(2,1), "b"); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(2,2), "c"); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(2,3), "d"); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(3,0), true); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(3,1), false); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(3,2), true); - Assert.assertEquals(((RDataFrame)testA.get(4)).get(3,3), false); - Assert.assertEquals(testA.getName(0),"one"); - Assert.assertEquals(testA.getName(1),"two"); - Assert.assertEquals(testA.getName(2),"three"); - Assert.assertEquals(testA.getName(3),"four"); - Assert.assertEquals(testA.getName(4),"five"); - engine.setAutoCommit(true); - - } - - @Test - public void testArrayBool() throws Exception { - engine.voidEval("a<-c(TRUE,FALSE,TRUE)"); - Boolean[] testBoolArray = (Boolean[]) engine.eval("a"); - Assert.assertTrue(testBoolArray[0]); - Assert.assertFalse(testBoolArray[1]); - Assert.assertTrue(testBoolArray[2]); - } - - @Test - public void testWorkingDirectory() throws Exception { - File workingDirectory = new File("/tmp"); - engine.setwd(workingDirectory); - File testWorkingDirectory = engine.getwd(); - Assert.assertEquals(workingDirectory.getAbsolutePath(), - testWorkingDirectory.getAbsolutePath()); - } - - @Test - public void testRData() throws Exception { - File workingdir = new File("/tmp"); - engine.voidEval("a<-5.0"); - engine.saveRData(workingdir); - engine.remove("a"); - engine.loadRData(workingdir); - Assert.assertEquals(5.0, engine.eval("a")); - } - - @Test - public void testDputDget() throws Exception { - File workingdir = new File("/tmp"); - File testingFile = new File("/tmp/testfile"); - - // test method using the workingdir - engine.voidEval("a<-5.0"); - engine.setwd(workingdir); - engine.dput("a", "testDputDgetfile"); - engine.remove("a"); - engine.dget("a", "testDputDgetfile"); - Assert.assertEquals(5.0, engine.eval("a")); - - workingdir = new File("/"); - //test method using absolute path - engine.setwd(workingdir); - engine.voidEval("a<-6.0"); - engine.dput("a", testingFile); - engine.remove("a"); - engine.dget("a", testingFile); - Assert.assertEquals(6.0, engine.eval("a")); - File testWorkingDirectory = engine.getwd(); - Assert.assertEquals(workingdir.getAbsolutePath(), - testWorkingDirectory.getAbsolutePath()); - } - - @Test - public void testRemove() throws Exception { - engine.voidEval("a<-6.0"); - Assert.assertEquals(6.0, engine.eval("a")); - engine.remove("a"); - Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); - } - - @Test - public void testMvCp() throws Exception { - //Test only mv as mv uses cp. - engine.voidEval("a<-5.0"); - engine.remove("b"); - engine.mv("a", "b"); - Assert.assertEquals(5.0, engine.eval("b")); - Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); - } - - @Test - public void testLsClearSession() throws Exception { - //Test only ClearSession as it uses ls - engine.voidEval("a<-5.0"); - engine.voidEval("b<-5.0"); - engine.voidEval("d<-5.0"); - engine.voidEval("e<-5.0"); - engine.voidEval("f<-5.0"); - engine.clearSession(); - Assert.assertFalse((Boolean) engine.eval("exists(\"a\")")); - Assert.assertFalse((Boolean) engine.eval("exists(\"b\")")); - Assert.assertFalse((Boolean) engine.eval("exists(\"d\")")); - Assert.assertFalse((Boolean) engine.eval("exists(\"e\")")); - Assert.assertFalse((Boolean) engine.eval("exists(\"f\")")); - } - - @Test - public void testAutoCommitFalse() throws Exception { - engine.clearSession(); - engine.setAutoCommit(false); - engine.voidEval("a<-5.0"); - engine.voidEval("a<-a+5.0"); - engine.voidEval("b<-5.0"); - engine.voidEval("d<-5.0"); - engine.voidEval("e<-5.0"); - engine.voidEval("f<-5.0"); - engine.commit(); - Assert.assertEquals(10.0, engine.eval("a")); - Assert.assertEquals(5.0, engine.eval("b")); - Assert.assertEquals(5.0, engine.eval("d")); - Assert.assertEquals(5.0, engine.eval("e")); - Assert.assertEquals(5.0, engine.eval("f")); - } - - @Test - public void testThrowException() throws Exception { - engine.clearSession(); - //Test that the exception is normally thrown in voidEval - try { - engine.voidEval("a<-b"); - Assert.fail("Exception should have been thrown at this point"); - } catch (RException e) { - log.info(e.getMessage()); - Assert.assertTrue( - e.getMessage().contains("objet \'b\' introuvable")); - } - - engine.clearSession(); - try { - engine.eval("a"); - Assert.fail("Exception should have been thrown at this point"); - } catch (RException e) { - Assert.assertTrue( - e.getMessage().contains("objet \'a\' introuvable")); - } - } - - @Test - public void testNonRegretionOnErrorFromR() throws Exception{ - try{ - engine.voidEval("dfresults<-data.frame(c(1,2,3),c(4,5,6))"); - } catch (NullPointerException npe){ - Assert.fail("Error should not have been thrown : " + npe); - } - } - - @Test - public void testListWithNullNames() throws Exception { - RList b = new RList(engine); - try { - b = (RList) engine.eval("b<-list(\"b\",\"a\")"); - b.setVariable("b"); - } catch (NullPointerException npe) { - Assert.fail("Error should not have been thrown : " + npe); - } - - Assert.assertEquals("b", b.get(0)); - Assert.assertEquals("a", b.get(1)); - - } - - @Test - public void testScripts() throws Exception { - double d = (Double) engine.evalScript("t<-sin(0)\nt"); - Assert.assertEquals(0.0, d, 0.001); - } - - @Test - public void testGraphics() throws Exception { - - File workingDirectory = new File("/tmp"); - engine.setwd(workingDirectory); - - engine.plot("test", "seq(1,10)", null, null, null, null, null, null, null); - File pictureFile = new File("/tmp/test.jpg"); - Assert.assertTrue(pictureFile.exists()); - //engine.eval("plot(seq(1,10))"); - } - - } // NetTest

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r236 - in trunk/src: main/java/org/nuiton/j2r test/java/org/nuiton/j2r
by jcouteau＠users.nuiton.org Oct. 18, 2010

Oct. 18, 2010

Author: jcouteau Date: 2010-10-18 11:43:32 +0200 (Mon, 18 Oct 2010) New Revision: 236 Url: http://nuiton.org/repositories/revision/nuiton-j2r/236 Log: Proper test skipping when no R environment present Modified: trunk/src/main/java/org/nuiton/j2r/RProxy.java trunk/src/test/java/org/nuiton/j2r/DataframeTest.java trunk/src/test/java/org/nuiton/j2r/JNITest.java trunk/src/test/java/org/nuiton/j2r/ListTest.java trunk/src/test/java/org/nuiton/j2r/NetTest.java Modified: trunk/src/main/java/org/nuiton/j2r/RProxy.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/RProxy.java 2010-10-18 09:21:30 UTC (rev 235) +++ trunk/src/main/java/org/nuiton/j2r/RProxy.java 2010-10-18 09:43:32 UTC (rev 236) @@ -669,5 +669,31 @@ engine.plot(filename, x, y, type, main, sub, xlab, ylab, asp); } + /** + * To know if the engine interfaced is a RNetEngine. + * + * @return true if the engine interfaced is a RNetEngine. + */ + public boolean isNet() { + if (engine != null) { + return engine instanceof RNetEngine; + } else { + return false; + } + } + + /** + * To know if the engine interfaced is a RJniEngine. + * + * @return true if the engine interfaced is a RJniEngine. + */ + public boolean isJni() { + if (engine != null) { + return engine instanceof RJniEngine; + } else { + return false; + } + } + } //RProxy Modified: trunk/src/test/java/org/nuiton/j2r/DataframeTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/DataframeTest.java 2010-10-18 09:21:30 UTC (rev 235) +++ trunk/src/test/java/org/nuiton/j2r/DataframeTest.java 2010-10-18 09:43:32 UTC (rev 236) @@ -37,6 +37,7 @@ import org.junit.Assert; import org.junit.Assume; import org.junit.Before; +import org.junit.BeforeClass; import org.junit.Test; import org.nuiton.j2r.types.RDataFrame; @@ -46,17 +47,23 @@ private REngine engine; - @Before - public void setUp() throws Exception { - if (engine == null) { - try { - engine = new RProxy(); - } catch (RException eee){ - Assume.assumeTrue(false); + @BeforeClass + public static void tryREnv(){ + try { + new RProxy(); + } catch (RException eee) { + if (log.isErrorEnabled()) { + log.error("No R environment found to run tests. Skip"); } + Assume.assumeTrue(false); } } + @Before + public void setUp() throws Exception { + engine = new RProxy(); + } + @After public void tearDown() throws Exception { if (engine != null){ Modified: trunk/src/test/java/org/nuiton/j2r/JNITest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-10-18 09:21:30 UTC (rev 235) +++ trunk/src/test/java/org/nuiton/j2r/JNITest.java 2010-10-18 09:43:32 UTC (rev 236) @@ -41,6 +41,7 @@ import org.junit.Assert; import org.junit.Assume; import org.junit.Before; +import org.junit.BeforeClass; import org.junit.Test; import org.nuiton.j2r.jni.RJniEngine; import org.nuiton.j2r.types.RDataFrame; @@ -56,6 +57,37 @@ private REngine engine; private String savedRType; + @BeforeClass + public static void tryREnv() { + + RProxy testedEngine = null; + + //Force R.type to net + String savedRType = System.getProperty("R.type", ""); + System.setProperty("R.type", "jni"); + + try { + testedEngine = new RProxy(); + } catch (RException eee) { + if (log.isErrorEnabled()) { + log.error("No R environment found to run tests. Skip"); + } + Assume.assumeTrue(false); + } + + //Restore old R.type + System.setProperty("R.type", savedRType); + + if (testedEngine != null) { + Assume.assumeTrue(testedEngine.isJni()); + if (log.isErrorEnabled()) { + log.error("No JRI environment found. Skip tests."); + } + } + + + } + @Before public void setUp() throws Exception { LutinTimer init = new LutinTimer(); Modified: trunk/src/test/java/org/nuiton/j2r/ListTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-10-18 09:21:30 UTC (rev 235) +++ trunk/src/test/java/org/nuiton/j2r/ListTest.java 2010-10-18 09:43:32 UTC (rev 236) @@ -31,6 +31,7 @@ import org.junit.Assert; import org.junit.Assume; import org.junit.Before; +import org.junit.BeforeClass; import org.junit.Test; import org.nuiton.j2r.types.RList; @@ -47,17 +48,23 @@ private REngine engine; - @Before - public void setUp() throws Exception { - if (engine == null) { - try { - engine = new RProxy(); - } catch (RException eee) { - Assume.assumeTrue(false); + @BeforeClass + public static void tryREnv() { + try { + new RProxy(); + } catch (RException eee) { + if (log.isErrorEnabled()) { + log.error("No R environment found to run tests. Skip"); } + Assume.assumeTrue(false); } } + @Before + public void setUp() throws Exception { + engine = new RProxy(); + } + @After public void tearDown() throws Exception { if (engine != null) { Modified: trunk/src/test/java/org/nuiton/j2r/NetTest.java =================================================================== --- trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-10-18 09:21:30 UTC (rev 235) +++ trunk/src/test/java/org/nuiton/j2r/NetTest.java 2010-10-18 09:43:32 UTC (rev 236) @@ -51,11 +51,11 @@ import org.junit.Assert; import org.junit.Assume; import org.junit.Before; +import org.junit.BeforeClass; import org.junit.Test; import org.nuiton.j2r.net.RNetEngine; import org.nuiton.j2r.types.RDataFrame; import org.nuiton.j2r.types.RList; -import org.rosuda.REngine.Rserve.RserveException; public class NetTest { @@ -63,6 +63,37 @@ private REngine engine; private String savedRType; + @BeforeClass + public static void tryREnv() { + + RProxy testedEngine= null; + + //Force R.type to net + String savedRType = System.getProperty("R.type", ""); + System.setProperty("R.type", "net://:6311"); + + try { + testedEngine = new RProxy(); + } catch (RException eee) { + if (log.isErrorEnabled()) { + log.error("No R environment found to run tests. Skip"); + } + Assume.assumeTrue(false); + } + + //Restore old R.type + System.setProperty("R.type", savedRType); + + if (testedEngine != null){ + Assume.assumeTrue(testedEngine.isNet()); + if (log.isErrorEnabled()) { + log.error("No Rserve environment found. Skip tests."); + } + } + + + } + @Before public void setUp() throws Exception { LutinTimer init = new LutinTimer();

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