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Uwe Bohne

2013-Nov-19 09:11 UTC

[R] Installation problems: Linux Java and R not working together

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?

   Warnmeldung:

   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
   Done.



   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
   mode
   * 2            /usr/lib/jdk_Oracle/bin/java              3         manual
   mode
     3            /usr/lib/jvm/jre-1.5.0-gcj/bin/java       1500      manual
   mode
     4            /usr/lib/jvm/jre-1.7.0-openjdk/bin/java   17147     manual
   mode
   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

   Uwe

Prof Brian Ripley

2013-Nov-19 09:37 UTC

head link

[R] Installation problems: Linux Java and R not working together

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?
>
>     Warnmeldung:
>
>     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
>     Done.
>
>
>
>     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
>     mode
>     * 2            /usr/lib/jdk_Oracle/bin/java              3        
manual
>     mode
>       3            /usr/lib/jvm/jre-1.5.0-gcj/bin/java       1500     
manual
>     mode
>       4            /usr/lib/jvm/jre-1.7.0-openjdk/bin/java   17147    
manual
>     mode
>     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
>
>     Uwe
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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

R help - Nov 2013 - Installation problems: Linux Java and R not working together

[R] Installation problems: Linux Java and R not working together

[R] Installation problems: Linux Java and R not working together