October 2013 - Nuiton-j2r-commits - mailman.cloud.codelutin.com

r295 - in trunk/src/main: java/org/nuiton/j2r/jni resources
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 23:43:33 +0100 (Thu, 31 Oct 2013) New Revision: 295 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/295 Log: fixes #2883: Autoload nativelibs depending on java platform and arch Added: trunk/src/main/java/org/nuiton/j2r/jni/RNative.java trunk/src/main/resources/linux-x86-64/ trunk/src/main/resources/linux-x86/ trunk/src/main/resources/win32-x86-64/ Removed: trunk/src/main/resources/linux-amd64/ trunk/src/main/resources/linux-i386/ trunk/src/main/resources/win32-amd64/ Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java Modified: trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2013-10-31 21:06:25 UTC (rev 294) +++ trunk/src/main/java/org/nuiton/j2r/jni/RJniEngine.java 2013-10-31 22:43:33 UTC (rev 295) @@ -5,7 +5,7 @@ * $Id$ * $HeadURL$ * %% - * Copyright (C) 2006 - 2012 CodeLutin, Chatellier Eric + * Copyright (C) 2006 - 2013 CodeLutin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -50,7 +50,7 @@ */ public class RJniEngine extends REngineAbstract implements REngine { - private Log log = LogFactory.getLog(RJniEngine.class); + private static Log log = LogFactory.getLog(RJniEngine.class); /** * Rengine is made to be static */ @@ -84,11 +84,13 @@ //jriLoaded is false is rJava did not find jri library if (!Rengine.jriLoaded) { - if (log.isErrorEnabled()) { - log.error( - "Cannot find jri library, make sure it is correctly installed"); + if (!RNative.loadNativeRLibraryFromClasspath()) { + if (log.isErrorEnabled()) { + log.error( + "Cannot find jri library, make sure it is correctly installed"); + } + return false; } - return false; } engine = new Rengine(args, false, null); Added: trunk/src/main/java/org/nuiton/j2r/jni/RNative.java =================================================================== --- trunk/src/main/java/org/nuiton/j2r/jni/RNative.java (rev 0) +++ trunk/src/main/java/org/nuiton/j2r/jni/RNative.java 2013-10-31 22:43:33 UTC (rev 295) @@ -0,0 +1,170 @@ +/* + * #%L + * Nuiton Java-2-R library + * + * $Id: RJniEngine.java 271 2012-02-09 10:27:30Z echatellier $ + * $HeadURL: http://svn.nuiton.org/svn/nuiton-j2r/trunk/src/main/java/org/nuiton/j2r/jni… $ + * %% + * Copyright (C) 2006 - 2013 CodeLutin, Chatellier Eric + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU 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 Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ +package org.nuiton.j2r.jni; + +import java.io.File; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +/** + * Backport code from JNA project to load native file from classpath. + * + * @see https://github.com/twall/jna/blob/master/src/com/sun/jna/Native.java + * + * @author Chatellier Eric + */ +public class RNative { + + private static Log log = LogFactory.getLog(RNative.class); + + public static final String RESOURCE_PREFIX; + + public static final boolean IS_WINDOWS; + + public static final boolean IS_LINUX; + + static { + String osName = System.getProperty("os.name"); + IS_WINDOWS = osName.startsWith("Windows"); + IS_LINUX = osName.startsWith("Linux"); + RESOURCE_PREFIX = getNativeLibraryResourcePrefix(); + } + + static String getNativeLibraryResourcePrefix() { + return getNativeLibraryResourcePrefix(System.getProperty("os.arch")); + } + + /** + * Generate a canonical String prefix based on the given OS + * type/arch/name. + * + * @param arch from <code>os.arch</code> System property + * @param name from <code>os.name</code> System property + */ + static String getNativeLibraryResourcePrefix(String arch) { + String osPrefix; + arch = arch.toLowerCase().trim(); + if ("i386".equals(arch)) { + arch = "x86"; + } + else if ("x86_64".equals(arch) || "amd64".equals(arch)) { + arch = "x86-64"; + } + + if (IS_WINDOWS) { + osPrefix = "win32-" + arch; + } else if (IS_LINUX) { + osPrefix = "linux-" + arch; + } else { + throw new UnsatisfiedLinkError("Unsupported plaform/arch"); + } + + return osPrefix; + } + + static boolean loadNativeRLibraryFromClasspath() { + boolean result = false; + try { + String libName = "/" + RESOURCE_PREFIX + "/" + System.mapLibraryName("jri"); + File lib = extractFromResourcePath(libName, RNative.class.getClassLoader()); + if (lib == null) { + if (lib == null) { + throw new UnsatisfiedLinkError("Could not find R native support"); + } + } + + System.load(lib.getAbsolutePath()); + result = true; + if (log.isInfoEnabled()) { + log.info("Loaded jri native library from classpath (" + libName + ")"); + } + } catch(IOException e) { + throw new UnsatisfiedLinkError(e.getMessage()); + } + return result; + } + + /** + * Attempt to extract a native library from the resource path using the + * given class loader. + * @param name Base name of native library to extract. May also be an + * absolute resource path (i.e. starts with "/"), in which case the + * no transformations of the library name are performed. If only the base + * name is given, the resource path is attempted both with and without + * {@link Platform#RESOURCE_PREFIX}, after mapping the library name via + * {@link NativeLibrary#mapSharedLibraryName(String)}. + * @param loader Class loader to use to load resources + * @return File indicating extracted resource on disk + * @throws IOException if resource not found + */ + public static File extractFromResourcePath(String name, ClassLoader loader) throws IOException { + if (loader == null) { + loader = Thread.currentThread().getContextClassLoader(); + // Context class loader is not guaranteed to be set + if (loader == null) { + loader = RNative.class.getClassLoader(); + } + } + + String resourcePath = name; + if (resourcePath.startsWith("/")) { + resourcePath = resourcePath.substring(1); + } + InputStream is = loader.getResourceAsStream(resourcePath); + if (is == null) { + throw new IOException("Can't obtain InputStream for " + resourcePath); + } + + File lib = null; + FileOutputStream fos = null; + try { + // Suffix is required on windows, or library fails to load + // Let Java pick the suffix, except on windows, to avoid + // problems with Web Start. + lib = File.createTempFile("nuiton-j2r-", IS_WINDOWS ? ".dll" : null); + lib.deleteOnExit(); + fos = new FileOutputStream(lib); + int count; + byte[] buf = new byte[1024]; + while ((count = is.read(buf, 0, buf.length)) > 0) { + fos.write(buf, 0, count); + } + } + catch(IOException e) { + throw new IOException("Failed to create temporary file for " + name + " library: " + e.getMessage()); + } + finally { + try { is.close(); } catch(IOException e) { } + if (fos != null) { + try { fos.close(); } catch(IOException e) { } + } + } + return lib; + } +}

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r294 - in trunk: . doc
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 22:06:25 +0100 (Thu, 31 Oct 2013) New Revision: 294 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/294 Log: Move info to readme file Removed: trunk/doc/rJava.txt Modified: trunk/README.txt Modified: trunk/README.txt =================================================================== --- trunk/README.txt 2013-10-31 21:04:39 UTC (rev 293) +++ trunk/README.txt 2013-10-31 21:06:25 UTC (rev 294) @@ -1,2 +1,24 @@ +Nuiton-J2R +========== + +Build +----- To deploy new version of pom: mvn deploy To install localy: mvn install + +rJava +----- + +Windows +~~~~~~~ +http://cran.r-project.org/bin/windows/contrib/2.10/rJava_0.6-2.zip +http://cran.r-project.org/bin/windows64/contrib/2.11/rJava_0.8-5.zip + +Linux +~~~~~ +http://www.rforge.net/rJava/files/ + + ./configure + make + + \ No newline at end of file Deleted: trunk/doc/rJava.txt =================================================================== --- trunk/doc/rJava.txt 2013-10-31 21:04:39 UTC (rev 293) +++ trunk/doc/rJava.txt 2013-10-31 21:06:25 UTC (rev 294) @@ -1,13 +0,0 @@ -Windows -------- -http://cran.r-project.org/bin/windows/contrib/2.10/rJava_0.6-2.zip -http://cran.r-project.org/bin/windows64/contrib/2.11/rJava_0.8-5.zip - -Linux ------ -http://www.rforge.net/rJava/files/ - - ./configure - make - -

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r293 - in trunk/src/main/resources: . linux-amd64 linux-i386 win32-amd64 win32-x86
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 22:04:39 +0100 (Thu, 31 Oct 2013) New Revision: 293 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/293 Log: fixes #1564: Move dll, so, to match platform-arch layout Added: trunk/src/main/resources/linux-amd64/ trunk/src/main/resources/linux-i386/ trunk/src/main/resources/linux-i386/libjri.so trunk/src/main/resources/win32-amd64/ trunk/src/main/resources/win32-amd64/jri.dll trunk/src/main/resources/win32-x86/ trunk/src/main/resources/win32-x86/jri.dll Removed: trunk/src/main/resources/jri.dll trunk/src/main/resources/libjri.so trunk/src/main/resources/linux-amd64/jri.dll trunk/src/main/resources/x64/ Deleted: trunk/src/main/resources/jri.dll =================================================================== (Binary files differ) Deleted: trunk/src/main/resources/libjri.so =================================================================== (Binary files differ) Deleted: trunk/src/main/resources/linux-amd64/jri.dll =================================================================== (Binary files differ) Copied: trunk/src/main/resources/linux-i386/libjri.so (from rev 288, trunk/src/main/resources/libjri.so) =================================================================== (Binary files differ) Copied: trunk/src/main/resources/win32-amd64/jri.dll (from rev 288, trunk/src/main/resources/x64/jri.dll) =================================================================== (Binary files differ) Copied: trunk/src/main/resources/win32-x86/jri.dll (from rev 288, trunk/src/main/resources/jri.dll) =================================================================== (Binary files differ)

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r292 - trunk
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 21:59:03 +0100 (Thu, 31 Oct 2013) New Revision: 292 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/292 Log: Remove 'library' from lib name Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2013-10-31 20:55:15 UTC (rev 291) +++ trunk/pom.xml 2013-10-31 20:59:03 UTC (rev 292) @@ -126,7 +126,7 @@   - <name>Nuiton Java-2-R library</name> + <name>Nuiton Java-2-R</name> <description>Librairie permettant d'utiliser R en Java, que ce soit par le Network ou en JNI. </description>

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r291 - trunk
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 21:55:15 +0100 (Thu, 31 Oct 2013) New Revision: 291 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/291 Log: Update pom, version, etc... Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2013-10-31 20:54:59 UTC (rev 290) +++ trunk/pom.xml 2013-10-31 20:55:15 UTC (rev 291) @@ -6,7 +6,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 2006 - 2012 CodeLutin, Chatellier Eric + Copyright (C) 2006 - 2013 CodeLutin, Chatellier Eric %% This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as @@ -23,7 +23,7 @@ <http://www.gnu.org/licenses/gpl-3.0.html>. #L% --> -<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> +<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"> <modelVersion>4.0.0</modelVersion> @@ -34,11 +34,11 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmineAndCentral</artifactId> - <version>3.4.7</version> + <version>4.1</version> </parent> <artifactId>nuiton-j2r</artifactId> - <version>1.0.3-SNAPSHOT</version> + <version>1.1-SNAPSHOT</version> <developers> <developer>

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r290 - in trunk: . doc src/main/resources
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 21:54:59 +0100 (Thu, 31 Oct 2013) New Revision: 290 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/290 Log: fixes #2881: Remove jri-sources from resources Added: trunk/doc/ trunk/doc/JRI-sources.zip trunk/doc/rJava.txt Removed: trunk/src/main/resources/JRI-sources.zip trunk/src/main/resources/rJava.txt Copied: trunk/doc/JRI-sources.zip (from rev 288, trunk/src/main/resources/JRI-sources.zip) =================================================================== (Binary files differ) Copied: trunk/doc/rJava.txt (from rev 288, trunk/src/main/resources/rJava.txt) =================================================================== --- trunk/doc/rJava.txt (rev 0) +++ trunk/doc/rJava.txt 2013-10-31 20:54:59 UTC (rev 290) @@ -0,0 +1,13 @@ +Windows +------- +http://cran.r-project.org/bin/windows/contrib/2.10/rJava_0.6-2.zip +http://cran.r-project.org/bin/windows64/contrib/2.11/rJava_0.8-5.zip + +Linux +----- +http://www.rforge.net/rJava/files/ + + ./configure + make + + Deleted: trunk/src/main/resources/JRI-sources.zip =================================================================== (Binary files differ) Deleted: trunk/src/main/resources/rJava.txt =================================================================== --- trunk/src/main/resources/rJava.txt 2013-10-31 20:51:56 UTC (rev 289) +++ trunk/src/main/resources/rJava.txt 2013-10-31 20:54:59 UTC (rev 290) @@ -1,13 +0,0 @@ -Windows -------- -http://cran.r-project.org/bin/windows/contrib/2.10/rJava_0.6-2.zip -http://cran.r-project.org/bin/windows64/contrib/2.11/rJava_0.8-5.zip - -Linux ------ -http://www.rforge.net/rJava/files/ - - ./configure - make - -

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r289 - trunk
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 21:51:56 +0100 (Thu, 31 Oct 2013) New Revision: 289 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/289 Log: svn:ignore Modified: trunk/ Property changes on: trunk ___________________________________________________________________ Modified: svn:ignore - target .classpath .project .settings *.iml *.ipr nbactions.xml nb-configuration.xml + target .classpath .project .settings *.iml *.ipr nbactions.xml nb-configuration.xml .idea

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r288 - trunk/src/main/resources
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 21:51:20 +0100 (Thu, 31 Oct 2013) New Revision: 288 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/288 Log: Remove log4j.properties from main resources Removed: trunk/src/main/resources/log4j.properties Deleted: trunk/src/main/resources/log4j.properties =================================================================== --- trunk/src/main/resources/log4j.properties 2013-10-31 20:50:47 UTC (rev 287) +++ trunk/src/main/resources/log4j.properties 2013-10-31 20:51:20 UTC (rev 288) @@ -1,32 +0,0 @@ -### -# #%L -# Nuiton Java-2-R library -# -# $Id$ -# $HeadURL$ -# %% -# Copyright (C) 2006 - 2012 CodeLutin, Chatellier Eric -# %% -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU 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 Public License for more details. -# -# You should have received a copy of the GNU General Public -# License along with this program. If not, see -# <http://www.gnu.org/licenses/gpl-3.0.html>. -# #L% -### -# Global logging configuration -log4j.rootLogger=INFO, stdout -# Console output... -log4j.appender.stdout=org.apache.log4j.ConsoleAppender -log4j.appender.stdout.layout=org.apache.log4j.PatternLayout -log4j.appender.stdout.layout.ConversionPattern=%5p [%t] (%F:%L) %M - %m%n -# package level -log4j.logger.org.nuiton.j2r=INFO

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r287 - trunk
by echatellier＠users.nuiton.org 31 Oct '13

31 Oct '13

Author: echatellier Date: 2013-10-31 21:50:47 +0100 (Thu, 31 Oct 2013) New Revision: 287 Url: http://nuiton.org/projects/nuiton-j2r/repository/revisions/287 Log: Remove changelog file Removed: trunk/changelog.txt Deleted: trunk/changelog.txt =================================================================== --- trunk/changelog.txt 2013-02-18 14:21:20 UTC (rev 286) +++ trunk/changelog.txt 2013-10-31 20:50:47 UTC (rev 287) @@ -1,17 +0,0 @@ -nuiton-j2r (1.0.1) unstable; urgency=low - * add the RDataFrame data type - * add the recuperation of errors from R - -lutinj2r (0.3) unstable; urgency=low - * use lutinproject 3.4 - * use JRI 0.7 - * use Rserve 0.6 - * increase the number or R expressions handled - -lutinj2r (0.2) unstable; urgency=low - - * LGPL v3 - * Update site generation - * Maven2 layout - * UTF-8 - * Update pom \ No newline at end of file

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