[R] JGR / linux

Tue Jun 3 14:08:05 CEST 2008

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-1.6.0.03/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:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/lib:/usr/lib
JNI linker flags : -L$(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-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux

Updating Java configuration in /etc/R
Done.

$ 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

* Installing *source* package 'JavaGD' ...
checking for gcc... gcc-4.2 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.2 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.2 -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for select... yes
checking for socket... yes
checking Java support in R... present:
interpreter : '/usr/bin/java'
cpp flags : '-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux'
java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64/server
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/lib/amd64
-L/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include
-I/usr/lib/jvm/java-6-sun-1.6.0.03/jre/../include/linux -Iinclude -fpic -g
-O2 -c javaGD.c -o javaGD.o
In file included from javaGD.h:12,
from javaGD.c:23:
/usr/share/R/include/R_ext/GraphicsEngine.h:150: error: expected
specifier-qualifier-list before ‘NewDevDesc’
/usr/share/R/include/R_ext/GraphicsEngine.h:224: error: expected ‘)’ before
‘*’ token
/usr/share/R/include/R_ext/GraphicsEngine.h:231: error: expected declaration
specifiers or ‘...’ before ‘NewDevDesc’
javaGD.c: In function ‘Rf_addJavaGDDevice’:
javaGD.c:215: warning: implicit declaration of function ‘GEcreateDevDesc’
javaGD.c:215: warning: assignment makes pointer from integer without a cast
javaGD.c: In function ‘reloadJavaGD’:
javaGD.c:233: error: ‘GEDevDesc’ has no member named ‘dev’
javaGD.c: In function ‘javaGDobjectCall’:
javaGD.c:252: error: ‘GEDevDesc’ has no member named ‘dev’
javaGD.c: In function ‘javaGDresize’:
javaGD.c:269: error: ‘GEDevDesc’ has no member named ‘dev’
javaGD.c: In function ‘javaGDgetSize’:
javaGD.c:307: error: ‘GEDevDesc’ has no member named ‘dev’
make: *** [javaGD.o] Error 1
chmod: cannot access `/usr/local/lib/R/site-library/JavaGD/libs/*': No such
file or directory
ERROR: compilation failed for package 'JavaGD'
** Removing '/usr/local/lib/R/site-library/JavaGD'
* Installing *source* package 'JGR' ...
** R
** inst
** help
>>> Building/Updating help pages for package 'JGR'
Formats: text html latex example
jgr.addMenu text html latex example
jgr.addMenuItem text html latex example
jgr.addMenuSeperator text html latex example
supplements text html latex
** building package indices ...
* DONE (JGR)

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

>library(JGR)
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 3.1.1.20070321/gcc v4.1.3 
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