Différences
Ci-dessous, les différences entre deux révisions de la page.
Les deux révisions précédentes Révision précédente Prochaine révision | Révision précédente | ||
notes_compil_r [2008/01/20 10:42] – gerard | notes_compil_r [2017/08/25 09:56] (Version actuelle) – modification externe 127.0.0.1 | ||
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Ligne 1: | Ligne 1: | ||
- | ====== Version 2.4.1 ====== | + | ====== Installation de packages ====== |
+ | |||
+ | |||
+ | |||
+ | ===== package aplpack ===== | ||
+ | < | ||
+ | w2100-henry% ssh devel1@nemo | ||
+ | > echo $PATH | ||
+ | / | ||
+ | > setenv PATH / | ||
+ | > / | ||
+ | * Installing to library '/ | ||
+ | * Installing *source* package ' | ||
+ | ** R | ||
+ | ** inst | ||
+ | ** preparing package for lazy loading | ||
+ | Loading required package: tcltk | ||
+ | Error in firstlib(which.lib.loc, | ||
+ | Tcl/Tk support is not available on this system | ||
+ | Error: package ' | ||
+ | Execution halted | ||
+ | ERROR: lazy loading failed for package ' | ||
+ | ** Removing '/ | ||
+ | |||
+ | </ | ||
+ | |||
+ | ===== astuce pour installer un package dans le compte user ===== | ||
+ | il faut créer un répertoire tel qu' | ||
+ | < | ||
+ | nemo-henry% mkdir -p R/ | ||
+ | nemo-henry% pwd | ||
+ | / | ||
+ | nemo-henry% / | ||
+ | * Installing to library '/ | ||
+ | * Installing *source* package ' | ||
+ | ** R | ||
+ | ** inst | ||
+ | ** preparing package for lazy loading | ||
+ | Loading required package: tcltk | ||
+ | Loading Tcl/Tk interface ... done | ||
+ | ** help | ||
+ | >>> | ||
+ | | ||
+ | aplpack.package | ||
+ | bagplot | ||
+ | boxplot2D | ||
+ | faces | ||
+ | spin3R | ||
+ | stem.leaf | ||
+ | ** building package indices ... | ||
+ | * DONE (aplpack) | ||
+ | </ | ||
+ | |||
+ | ====== Notes de compilation ====== | ||
+ | |||
+ | |||
+ | ===== Version 2.4.1 ===== | ||
* [[http:// | * [[http:// | ||
- | ====== Version 2.6.1 ====== | + | ===== Version 2.6.1 ===== |
+ | |||
+ | ==== compilation avec gcc ==== | ||
+ | voir / | ||
+ | |||
+ | < | ||
+ | > ~/ | ||
+ | Java interpreter : / | ||
+ | Java version | ||
+ | Java home path : / | ||
+ | Java compiler | ||
+ | Java headers gen.: / | ||
+ | Java archive tool: / | ||
+ | Java library path: $(JAVA_HOME)/ | ||
+ | JNI linker flags : -L$(JAVA_HOME)/ | ||
+ | JNI cpp flags : -I/ | ||
+ | |||
+ | Updating Java configuration in / | ||
+ | Done. | ||
+ | |||
+ | </ | ||
+ | On utilise le gcc de blastwave, mais le f95 de SunStudio12: | ||
+ | < | ||
+ | > setenv PATH / | ||
+ | </ | ||
+ | puis on installe JGR: | ||
+ | < | ||
+ | > / | ||
+ | </ | ||
+ | |||
+ | ==== compilation sunstudio12 32 bits ==== | ||
Le script pour compiler | Le script pour compiler | ||
< | < | ||
Ligne 33: | Ligne 119: | ||
</ | </ | ||
- | Le check échoue!? | ||
- | Pour lancer, voir le script /bin/R26 | ||
- | ===== Problèmes ===== | ||
- | ==== avec JGR ==== | ||
- | < | ||
- | > library(JGR) | ||
- | Loading required package: rJava | ||
- | Loading required package: JavaGD | ||
- | Loading required package: iplots | ||
- | Java Accessibility Bridge for GNOME loaded. | ||
- | Please use the corresponding JGR launcher to start JGR. | ||
- | Run JGR() for details. You can also use JGR(update=TRUE) to update JGR. | ||
- | |||
- | > JGR() | ||
- | Starting JGR ... | ||
- | (You can use / | ||
- | > Exception in thread " | ||
- | at java.lang.ClassLoader.defineClass1(Native Method) | ||
- | at java.lang.ClassLoader.defineClass(ClassLoader.java: | ||
- | at java.security.SecureClassLoader.defineClass(SecureClassLoader.java: | ||
- | at java.net.URLClassLoader.defineClass(URLClassLoader.java: | ||
- | at java.net.URLClassLoader.access$100(URLClassLoader.java: | ||
- | at java.net.URLClassLoader$1.run(URLClassLoader.java: | ||
- | at java.security.AccessController.doPrivileged(Native Method) | ||
- | at java.net.URLClassLoader.findClass(URLClassLoader.java: | ||
- | at RJavaClassLoader.findClass(RJavaClassLoader.java: | ||
- | at java.lang.ClassLoader.loadClass(ClassLoader.java: | ||
- | at java.lang.ClassLoader.loadClass(ClassLoader.java: | ||
- | at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: | ||
- | at java.lang.Class.getDeclaredMethods0(Native Method) | ||
- | at java.lang.Class.privateGetDeclaredMethods(Class.java: | ||
- | at java.lang.Class.getMethod0(Class.java: | ||
- | at java.lang.Class.getMethod(Class.java: | ||
- | at RJavaClassLoader.bootClass(RJavaClassLoader.java: | ||
- | at RJavaClassLoader.main(RJavaClassLoader.java: | ||
- | |||
- | </ | ||
- | pourtant, il est installé: | ||
- | < | ||
- | > find / | ||
- | / | ||
- | </ | ||
- | |||
- | et la compilation: | ||
< | < | ||
/ | / | ||
Ligne 239: | Ligne 281: | ||
</ | </ | ||
+ | Le check échoue!? | ||
+ | Pour lancer, voir le script /bin/R26 | ||
Ligne 246: | Ligne 290: | ||
dans / | dans / | ||
+ | ===== R 2.7.1 avec studio 12 ===== | ||
+ | voir le répertoire / | ||
+ | |||
+ | < | ||
+ | setenv PATH / | ||
+ | </ | ||
+ | et le fichier do_work32.sh | ||
+ | \\ | ||
+ | les tests échouent, mais on peut faire l' | ||
+ | |||
+ | ===== Problèmes ===== | ||
+ | |||
+ | ==== avec JGR et Studio12 ==== | ||
+ | [[http:// | ||
+ | |||
+ | < | ||
+ | > library(JGR) | ||
+ | Loading required package: rJava | ||
+ | Loading required package: JavaGD | ||
+ | Loading required package: iplots | ||
+ | Java Accessibility Bridge for GNOME loaded. | ||
+ | |||
+ | |||
+ | Please use the corresponding JGR launcher to start JGR. | ||
+ | Run JGR() for details. You can also use JGR(update=TRUE) to update JGR. | ||
+ | |||
+ | > JGR() | ||
+ | Starting JGR ... | ||
+ | (You can use / | ||
+ | > Exception in thread " | ||
+ | at java.lang.ClassLoader.defineClass1(Native Method) | ||
+ | at java.lang.ClassLoader.defineClass(ClassLoader.java: | ||
+ | at java.security.SecureClassLoader.defineClass(SecureClassLoader.java: | ||
+ | at java.net.URLClassLoader.defineClass(URLClassLoader.java: | ||
+ | at java.net.URLClassLoader.access$100(URLClassLoader.java: | ||
+ | at java.net.URLClassLoader$1.run(URLClassLoader.java: | ||
+ | at java.security.AccessController.doPrivileged(Native Method) | ||
+ | at java.net.URLClassLoader.findClass(URLClassLoader.java: | ||
+ | at RJavaClassLoader.findClass(RJavaClassLoader.java: | ||
+ | at java.lang.ClassLoader.loadClass(ClassLoader.java: | ||
+ | at java.lang.ClassLoader.loadClass(ClassLoader.java: | ||
+ | at java.lang.ClassLoader.loadClassInternal(ClassLoader.java: | ||
+ | at java.lang.Class.getDeclaredMethods0(Native Method) | ||
+ | at java.lang.Class.privateGetDeclaredMethods(Class.java: | ||
+ | at java.lang.Class.getMethod0(Class.java: | ||
+ | at java.lang.Class.getMethod(Class.java: | ||
+ | at RJavaClassLoader.bootClass(RJavaClassLoader.java: | ||
+ | at RJavaClassLoader.main(RJavaClassLoader.java: | ||
+ | |||
+ | </ | ||
+ | pourtant, il est installé: | ||
+ | < | ||
+ | > find / | ||
+ | / | ||
+ | </ | ||
+ | |||
+ | Après avoir hacké le script de lancement (voir [[hacks]]), il y a un problème au lancement: | ||
+ | < | ||
+ | > bash / | ||
+ | Java Accessibility Bridge for GNOME loaded. | ||
+ | |||
+ | Cannot find JRI native library! | ||
+ | |||
+ | java.lang.UnsatisfiedLinkError: | ||
+ | at java.lang.ClassLoader$NativeLibrary.load(Native Method) | ||
+ | at java.lang.ClassLoader.loadLibrary0(ClassLoader.java: | ||
+ | at java.lang.ClassLoader.loadLibrary(ClassLoader.java: | ||
+ | at java.lang.Runtime.loadLibrary0(Runtime.java: | ||
+ | at java.lang.System.loadLibrary(System.java: | ||
+ | at org.rosuda.JGR.JGR.< | ||
+ | at org.rosuda.JGR.JGR.main(JGR.java: | ||
+ | at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) | ||
+ | at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: | ||
+ | at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java: | ||
+ | at java.lang.reflect.Method.invoke(Method.java: | ||
+ | at RJavaClassLoader.bootClass(RJavaClassLoader.java: | ||
+ | at RJavaClassLoader.main(RJavaClassLoader.java: | ||
+ | > | ||
+ | et pourtant, la lib est bien présente! | ||
+ | </ | ||
+ | voir [[http:// | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | ==== JGR et Java ==== | ||
+ | Ne marche pas avec java 1.5 livré avec l'os: | ||
+ | < | ||
+ | nemo-root% ls -l /usr/java | ||
+ | lrwxrwxrwx | ||
+ | |||
+ | </ | ||
+ | On installe la version 1.6 et on teste: | ||
+ | < | ||
+ | nemo-root% ls -l | ||
+ | total 12 | ||
+ | drwxr-xr-x | ||
+ | lrwxrwxrwx | ||
+ | lrwxrwxrwx | ||
+ | lrwxrwxrwx | ||
+ | nemo-root% cd /usr | ||
+ | /usr | ||
+ | nemo-root% rm java | ||
+ | rm: remove java (yes/no)? y | ||
+ | nemo-root% ln -s jdk/ | ||
+ | nemo-root% ls -l java | ||
+ | lrwxrwxrwx | ||
+ | > / | ||
+ | Java interpreter : / | ||
+ | Java version | ||
+ | Java home path : / | ||
+ | Java compiler | ||
+ | Java headers gen.: / | ||
+ | Java archive tool: / | ||
+ | Java library path: $(JAVA_HOME)/ | ||
+ | JNI linker flags : -L$(JAVA_HOME)/ | ||
+ | JNI cpp flags : -I/ | ||
+ | |||
+ | Updating Java configuration in / | ||
+ | Done. | ||
+ | |||
+ | </ | ||
+ | mais quand on le lance, plante: | ||
+ | < | ||
+ | Starting JGR ... | ||
+ | (You can use / | ||
+ | > Cannot find JRI native library! | ||
+ | |||
+ | java.lang.UnsatisfiedLinkError: | ||
+ | at java.lang.ClassLoader$NativeLibrary.load(Native Method) | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | |||
+ | ====== references ====== | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// |