Re: [R] Can't get R to recognize Java for rJava installation

2012-11-16 Thread gparab 
Also, remember when you use it to connect to a DB: Teradata or Orcale or
MySQLmake sure you have JRE running and relevant DB jars are loaded in
class path.
.jclassPath() => to check class paths
.jinit() => to run JRE




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Re: [R] Can't get R to recognize Java for rJava installation

2012-11-13 Thread gparab 
I had similar issue. This worked for me:
get in as root:

export JAVA_HOME="/usr/java/jdk1.6.0_37/jre"
export PATH=$PATH:$JAVA_HOME/bin

ln -sf usr/java/default/bin/javah /usr/bin/javah
ln -sf usr/java/default/bin/javap /usr/bin/javap
(basically make sure you have all java* binaries that you have under
usr/java/default/bin/ are also under /usr/bin/ as link. Follow how javac is
placed under /usr/bin/)

R CMD javareconf

now make sure you still have the JAVA_HOME and PATH variable intact as you
set it. Go to R and try installing "rJava" package, it should work.




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Re: [R] Can't get R to recognize Java for rJava installation

2012-04-13 Thread Waichler, Scott R 
Milan,

Merci.  I did find the javah file and put it in /usr/bin, where R can now find 
it.  
However, I still get a similar error message when trying to install rJava, i.e. 

configure: error: One or more Java configuration variables are not set.

The only field that doesn't have a value now are the cpp flags:

cpp flags   : ''

Could this be the problem now?  How can I set those, and what value should I 
give?

Scott Waichler

> So I guess you need to find out what package provides this file on your
> distribution (which you did not mention). First check the file is
> currently not present.
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Re: [R] Can't get R to recognize Java for rJava installation

2012-04-13 Thread Milan Bouchet-Valat 
Le jeudi 12 avril 2012 à 13:41 -0700, Waichler, Scott R a écrit :
> Hi, I am unable to install the package rJava.  I tried doing what the output 
> suggests, but it doesn't help.  How can I get R to find/recognize my Java 
> installation?  I am running R-2.15.0.
> 
> waichler@snow> sudo R CMD javareconf
> Java interpreter : /usr/bin/java
> Java version : 1.6.0_22
> Java home path   : /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre
> Java compiler: /usr/bin/javac
> Java headers gen.:
> Java archive tool: /usr/bin/jar
> Java library path: 
> $(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib
> JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 
> -L$(JAVA_HOME)/../lib/i386 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib 
> -ljvm
> JNI cpp flags:
> 
> Updating Java configuration in /usr/lib/R
> Done.
> 
> > install.packages(c("rJava"), dependencies = T, repos = 
> > "http://cran.fhcrc.org";)
> . . . 
> checking whether siglongjmp is declared... yes
> checking Java support in R... present:
> interpreter : '/usr/bin/java'
> archiver: '/usr/bin/jar'
> compiler: '/usr/bin/javac'
> header prep.: ''
> cpp flags   : ''
> java libs   : '-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/i386/client 
> -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/i386 
> -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/../lib/i386 
> -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
> configure: error: One or more Java configuration variables are not set.
> Make sure R is configured with full Java support (including JDK). Run
> R CMD javareconf
> as root to add Java support to R.
> 
> If you don't have root privileges, run
> R CMD javareconf -e
> to set all Java-related variables and then install rJava.
> 
> ERROR: configuration failed for package ÆrJavaÇ
> * removing Æ/usr/lib/R/library/rJavaÇ
It looks like you need "Java headers gen." to be set. Here on my box
(Fedora 16) it is:
Java headers gen.: /usr/bin/javah

So I guess you need to find out what package provides this file on your
distribution (which you did not mention). First check the file is
currently not present.


Cheers

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[R] Can't get R to recognize Java for rJava installation

2012-04-12 Thread Waichler, Scott R 
Hi, I am unable to install the package rJava.  I tried doing what the output 
suggests, but it doesn't help.  How can I get R to find/recognize my Java 
installation?  I am running R-2.15.0.

waichler@snow> sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_22
Java home path   : /usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre
Java compiler: /usr/bin/javac
Java headers gen.:
Java archive tool: /usr/bin/jar
Java library path: 
$(JAVA_HOME)/lib/i386/client:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386:/usr/java/packages/lib/i386:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -L$(JAVA_HOME)/lib/i386 
-L$(JAVA_HOME)/../lib/i386 -L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm
JNI cpp flags:

Updating Java configuration in /usr/lib/R
Done.

> install.packages(c("rJava"), dependencies = T, repos = 
> "http://cran.fhcrc.org";)
. . . 
checking whether siglongjmp is declared... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
archiver: '/usr/bin/jar'
compiler: '/usr/bin/javac'
header prep.: ''
cpp flags   : ''
java libs   : '-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/i386/client 
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/lib/i386 
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/../lib/i386 
-L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
configure: error: One or more Java configuration variables are not set.
Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R.

If you don't have root privileges, run
R CMD javareconf -e
to set all Java-related variables and then install rJava.

ERROR: configuration failed for package ÆrJavaÇ
* removing Æ/usr/lib/R/library/rJavaÇ

Thanks,
Scott Waichler
Senior Research Scientist
Hydrology Group, Energy & Environment Directorate
Pacific Northwest National Laboratory

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