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
[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