[R] Linux Java and R not working together
balu555 at gmx.de
Wed Nov 13 11:22:00 CET 2013
I almost tried for 3 days now to install rJava and package FSelector on my
Linux machine but couldn't do so.
I searched all the forums and tried some tricks ... but unfortunately
couldn't find any solution.
First of all I did try to install rJava in my rkward without any changes ,
that gave me the following error :
configure: error: One or more JNI types differ from the corresponding native
type. You may need to use non-standard compiler flags or a different
compiler in order to fix this.
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/uwe/.rkward/library/rJava’
In install.packages(pkgs = c("rJava"), lib = "/home/uwe/.rkward/library", :
Installation des Pakets ‘rJava’ hatte Exit-Status ungleich 0
So then I started searching and found a tip. I did run the following;
uwe at linux-k2a8:~> sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.7.0_45
Java home path : /usr/lib/jdk1.7.0_45/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
NOTE: Your JVM has a bogus java.library.path system property!
Trying a heuristic via sun.boot.library.path to find jvm library...
Java library path: $(JAVA_HOME)/lib/i386/client
JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
Updating Java configuration in /usr/lib/R
And also did check
uwe at linux-k2a8:~> java -version
java version "1.7.0_45"
Java(TM) SE Runtime Environment (build 1.7.0_45-b18)
Java HotSpot(TM) Server VM (build 24.45-b08, mixed mode)
uwe at linux-k2a8:~> sudo /usr/sbin/update-alternatives --config java
There are 4 choices for the alternative java (providing /usr/bin/java).
Selection Path Priority Status
0 /usr/lib/jvm/jre-1.7.0-openjdk/bin/java 17147 auto mode
1 /usr/java/latest/bin/java 1 manual
* 2 /usr/lib/jdk_Oracle/bin/java 3 manual
3 /usr/lib/jvm/jre-1.5.0-gcj/bin/java 1500 manual
4 /usr/lib/jvm/jre-1.7.0-openjdk/bin/java 17147 manual
Press enter to keep the current choice[*], or type selection number:
I absolutely don't know what is wrong with that setup since my Java seems to
have JDK and all the other things needed for R.
For your Information here my system:
uwe at linux-k2a8:~> uname -rm
uwe at linux-k2a8:~> cat /proc/version
Linux version 3.4.63-2.44-desktop (geeko at buildhost) (gcc version 4.7.1
20120723 [gcc-4_7-branch revision 189773] (S Linux) ) #1 SMP PREEMPT Wed Oct
2 11:18:32 UTC 2013 (d91a619)
I would be really thankful for any advise to get rJava (and FSelector)
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