[R] Installation problems: Linux Java and R not working together
Prof Brian Ripley
ripley at stats.ox.ac.uk
Tue Nov 19 10:37:10 CET 2013
First, read the posting guide. This is a question about compiled code
and belongs on R-devel.
Second, the answer will be in the config.log file for rJava which you
have not shown us. You need to download and unpack it, then run
R CMD INSTALL rJava
and look at rJava/config.log
If that is not sufficient clue, do follow up on R-devel.
On 19/11/2013 09:11, Uwe Bohne wrote:
> Dear community,
> 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
> 3.4.63-2.44-desktop i686
> 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)
> running soon.
> Best wishes
> R-help at r-project.org mailing list
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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