[R] help updating package rJava (on ubuntu)

[Karl Brand]

Simon,

Thanks alot for the further clarification. As i said some where in my 
lengthy explanation - i don't what of the myriad steps were needed, only 
that they were performed and i now have an up-to-date rJava.

Next time (actually coming up soon) i'll certainly be following the 
couple simple steps you suggest. Also good to know that Java 1.7 can be 
used with the latest R (which is all i intend to install).

Thanks again for the follow up,

Karl

On 02/20/2012 03:37 AM, Simon Urbanek wrote:
> On Feb 19, 2012, at 4:31 PM, Karl Brand wrote:
>
>> Hi Hasan,
>>
>> Success. For myself and FWIW to other useR's here's how i spent the sunny half of my sunday to achieve it :/
>>
>> Many thanks for your and Simon's input,
>>
>
> FWIW you should not need to set any custom settings if you system is properly configured (if you use Java 1.7 you may need R 2.14.0 or higher which works around some bugs in 1.7 binaries). On Debian/Ubuntu you just install your favorite JDK (Sun/Oracle or OpenJDK) and use 'sudo update-alternatives --config java' or 'sudo update-java-alternatives' (depending on the age of your system) to select the right one.
>
> The fact you you had to tweak PATH means that something is seriously broken or you did setup the alternatives configuration correctly.
>
> Cheers,
> Simon
>
>
>
>> Karl
>>
>> Since:
>>
>> $ javac -version
>>
>> returned nothing i believe you (and Simon) were right, i.e, it (and JDK) were missing on my system. Furthermore:
>>
>> $ sudo R CMD javareconf
>> Java interpreter : /usr/bin/java
>> Java version     : 1.6.0_23
>> Java home path   : /usr/lib/jvm/java-6-openjdk/jre
>> Java compiler    : not present
>> Java headers gen.:
>> Java archive tool:
>> Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
>> JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
>> JNI cpp flags    :
>>
>> Updating Java configuration in /etc/R
>> Done.
>>
>> Some things are clearly absent i.e.,
>> Java compiler    : not present
>> Java headers gen.:
>> Java archive tool:
>>
>> Now i have:
>>
>> $ javac -version
>> javac 1.6.0_23
>>
>> $ sudo R CMD javareconf
>> Java interpreter : /usr/bin/java
>> Java version     : 1.6.0_23
>> Java home path   : /usr/lib/jvm/java-6-openjdk/jre
>> Java compiler    : /usr/bin/javac
>> Java headers gen.: /usr/bin/javah
>> Java archive tool: /usr/bin/jar
>> Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/jni:/lib:/usr/lib
>> JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
>> JNI cpp flags    : -I$(JAVA_HOME)/../include
>>
>> Updating Java configuration in /etc/R
>> Done.
>>
>> Certainly i don't know exactly what was needed to achieve this. BUT - for posterities sake, this is what i did:
>>
>> ## purge and reinstall openjdk-6-jdk which turned outwasn't installed!
>> ## how this can be when i have a /usr/lib/jvm/java-6-openjdk full of
>> ## files i don't understand. Moreover since i had the previosu version
>> ## of rJava running fine!!!
>> $ sudo apt-get purge openjdk-6-jdk
>> <snip>
>> Package openjdk-6-jdk is not installed, so not removed
>> 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
>>
>> ## install openjdk-6-jdk
>> $ sudo apt-get install openjdk-6-jdk
>>
>> ## Per- http://ubuntuforums.org/showthread.php?t=1491846
>> ## added 2 entries to /etc/bash.bashrc file
>> $ gksudo gedit /etc/bash.bashrc
>>
>> ## entries were:
>> export JAVA_HOME=/usr/lib/jvm/java-6-openjdk/jre
>> export PATH=$PATH:$JAVA_HOME/bin
>>
>> ## note the addition of /jre for JAVA_HOME per-
>> ## http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing
>>
>> <saved bash.bashrc file then reloaded>
>>
>> $ source /etc/bash.bashrc
>>
>> ## confirmed
>> $ echo $JAVA_HOME
>> /usr/lib/jvm/java-6-openjdk/jre
>>
>> ## configured java
>> $ sudo R CMD javareconf
>>
>> I was then able to update rJava in a new R-session.
>>
>> Also note that per- http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing
>>
>> $ apt-get install r-cran-rjava
>>
>> did NOT enable me to update my rJava. Unless i buggered up something else along the way :/
>>
>>
>>
>>
>> On 02/18/2012 10:20 PM, Hasan Diwan wrote:
>>> On 18 February 2012 13:13, Karl Brand<k.brand at erasmusmc.nl>   wrote:
>>>> Thanks for yout fast response. Thing is - i managed to get Version 0.9-1
>>>> installed and fully functional. And
>>>>
>>>> $ locate jdk
>>>> returns too many entries to post here, so i'm pretty sure its on the
>>>> machine.
>>>
>>>
>>> What you want to look for is javac, not jdk. On my ubuntu system, this
>>> is to be found at /usr/lib/jvm/java-6-openjdk-i386/bin/javac
>>>>
>>>> So i'd like to know how i can ensure it's "registered in R". This i have no
>>>> idea how to do. I simply don't have enough R and linux experience. Also the
>>>> thread i mentioned
>>>> http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing
>>>> seems to be about pointing R at the right location of certain aspects of
>>>> Java. But lacks enough explicit details for myself to be able use.
>>>
>>> A previous response indicated R javareconf -- this is the only
>>> configuration you should need. Let me know if you have further
>>> problems.
>>
>> --
>> Karl Brand
>> Department of Genetics
>> Erasmus MC
>> Dr Molewaterplein 50
>> 3015 GE Rotterdam
>> T +31 (0)10 704 3455 |F +31 (0)10 704 4743 |M +31 (0)642 777 268
>>
>>
>

-- 
Karl Brand
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 704 3455 |F +31 (0)10 704 4743 |M +31 (0)642 777 268