[R] JGR / linux

From: g-h-d <erwann.rogard_at_gmail.com>
Date: Tue, 03 Jun 2008 05:08:05 -0700 (PDT)

Hi all,

i'm trying to install JGR on linux (see bottom), but it runs into errors. The bottom of the sequence below shows "JavaJD could not be found"

Any suggestion, please?

$ sudo apt-get install sun-java6-jdk

$ sudo update-alternatives --config java

There are 5 alternatives which provide `java'.

Selection Alternative

1 /usr/lib/jvm/java-1.5.0-sun/jre/bin/java
2 /usr/bin/gij-4.1
3 /usr/bin/gij-4.2
4 /usr/lib/jvm/java-gcj/jre/bin/java

+ 5 /usr/lib/jvm/java-7-icedtea/jre/bin/java

$sudo R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.6.0_03
Java home path : /usr/lib/jvm/java-6-sun- 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:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64
-L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib
-L/usr/lib -ljvm
JNI cpp flags : -I/usr/lib/jvm/java-6-sun-

Updating Java configuration in /etc/R

$ sudo R

R version 2.5.1 (2007-06-27)
Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

> install.packages('JGR', dep=TRUE)
Warning in install.packages("JGR", dep = TRUE) : argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
also installing the dependency ‘JavaGD’

trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JavaGD_0.5-1.tar.gz' Content type 'application/x-gzip' length 86505 bytes opened URL

downloaded 84Kb

trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/JGR_1.5-18.tar.gz' Content type 'application/x-gzip' length 426244 bytes opened URL

downloaded 416Kb The downloaded packages are in
Warning message:
installation of package 'JavaGD' had non-zero exit status in: install.packages("JGR", dep = TRUE)

Loading required package: rJava
Error: package 'JavaGD' required by 'JGR' could not be found

dell dimension E520/intel core duo 2/82G965 Integrated Graphics Controller/82562V 10/100 Network Connection ubuntu 7.10/gnome 2.21.1/eclipse SDK 3.2.2/cdt v4.1.3

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