[R] JGR/Deducer Installation

[Vikas Garud]

Hi,

Sorry if this is to wrong mailing list.  In that case, please point me
to correct mailing list.

Please also excuse rather long mail - I am not sure what piece of
information would be useful for anybody who could help me.

Couple of days back I had put a query about box-plots using GUI.  I
got some excellent suggestions.  One of them was to use JGR/Deducer.
It worked quite well for my needs.
Couple of days back there was a large on-line update in the system (I
use SuSE 11.4)  and JGR stopped working.  I tried uninstall/reinstall
of R, R-Devel, Java, from the SuSE repositories.  The versions are:

R version 2.13.0 (2011-04-13)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i686-pc-linux-gnu (32-bit)

Java: (All softwares, and their versions, installed from Java group)
ant  | 1.8.2-21.1
ant-antlr  | 1.8.2-21.1
ant-apache-bcel  | 1.8.2-21.1
ant-apache-bsf  | 1.8.2-21.1
ant-apache-log4j  | 1.8.2-21.1
ant-apache-oro  | 1.8.2-21.1
ant-apache-regexp  | 1.8.2-21.1
ant-apache-resolver  | 1.8.2-21.1
ant-commons-logging  | 1.8.2-21.1
ant-javadoc  | 1.8.2-21.1
ant-javamail  | 1.8.2-21.1
ant-jdepend  | 1.8.2-21.1
ant-jmf  | 1.8.2-21.1
ant-junit  | 1.8.2-21.1
ant-manual  | 1.8.2-21.1
ant-scripts  | 1.8.2-21.1
ant-swing  | 1.8.2-21.1
geronimo-j2ee-1_4-apis  | 1.2-11.5
jakarta-commons-logging  | 1.0.4-637.1
java-1_5_0-gcj-compat-devel  | 1.5.0.0-128.4
java-1_6_0-openjdk  | 1.6.0.0_b20.1.9.7-1.2.1
java-1_6_0-openjdk-devel  | 1.6.0.0_b20.1.9.7-1.2.1
java-1_6_0-openjdk-plugin  | 1.6.0.0_b20.1.9.7-1.2.1
javacc  | 4.0-226.1
jdepend  | 2.9.1-153.1
log4j  | 1.2.15-217.6
patterns-openSUSE-devel_java  | 11.4-6.9.1
xalan-j2  | 2.7.0-250.2
xerces-j2  | 2.8.1-247.3
xerces-j2-xml-apis  | 2.8.1-247.3
xerces-j2-xml-resolver  | 2.8.1-459.1
xml-commons-jaxp-1.1-apis  | 1.3.04-285.1
xml-commons-jaxp-1.3-apis  | 1.3.04-285.1
xml-commons-which10  | 1.3.04-285.1

Is anything missing?  Anything that should not be installed? Perhaps a
different version?

The messages while installing JGR are as follows

> install.packages (pkgs=c ("JGR"), lib="/home/vikas/R/i686-pc-linux-gnu-library/2.13", dependencies=TRUE)

also installing the dependencies ‘rJava’, ‘JavaGD’, ‘iplots’
* installing *source* package ‘rJava’ ...
checking for gcc... gcc -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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
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.: '/usr/bin/javah'
cpp flags   : '-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/server
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/i386
-L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types...
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/vikas/R/i686-pc-linux-gnu-library/2.13/rJava’

* installing *source* package ‘JavaGD’ ...
checking for gcc... gcc -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 -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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-1.6.0-openjdk-1.6.0/jre/../include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include/linux'
java libs   : '-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/server
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/i386
-L/usr/java/packages/lib/i386 -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 -std=gnu99 -I/usr/lib/R/include  -I/usr/local/include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include/linux -Iinclude
-fpic  -fomit-frame-pointer -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -c jGDtalk.c -o jGDtalk.o

jGDtalk.c:245:13: warning: ‘newJavaGD_Hold’ defined but not used

gcc -std=gnu99 -I/usr/lib/R/include  -I/usr/local/include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include/linux -Iinclude
-fpic  -fomit-frame-pointer -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -c javaGD.c -o javaGD.o
gcc -std=gnu99 -I/usr/lib/R/include  -I/usr/local/include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include
-I/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../include/linux -Iinclude
-fpic  -fomit-frame-pointer -fmessage-length=0 -O2 -Wall
-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables
-fasynchronous-unwind-tables -c s2u.c -o s2u.o
gcc -std=gnu99 -shared -L/usr/local/lib -o JavaGD.so jGDtalk.o
javaGD.o s2u.o -L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386/server
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/lib/i386
-L/usr/lib/jvm/java-1.6.0-openjdk-1.6.0/jre/../lib/i386
-L/usr/java/packages/lib/i386 -L/lib -L/usr/lib -ljvm -L/usr/lib/R/lib
-lR

installing to /home/vikas/R/i686-pc-linux-gnu-library/2.13/JavaGD/libs

** R

** inst

** preparing package for lazy loading

** help

*** installing help indices

** building package indices ...

** testing if installed package can be loaded

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/home/vikas/R/i686-pc-linux-gnu-library/2.13/JavaGD/libs/JavaGD.so':
  libjvm.so: cannot open shared object file: No such file or directory

Error: loading failed
Execution halted

ERROR: loading failed

* removing ‘/home/vikas/R/i686-pc-linux-gnu-library/2.13/JavaGD’

ERROR: dependency ‘rJava’ is not available for package ‘iplots’

* removing ‘/home/vikas/R/i686-pc-linux-gnu-library/2.13/iplots’

ERROR: dependencies ‘rJava’, ‘JavaGD’, ‘iplots’ are not available for
package ‘JGR’

* removing ‘/home/vikas/R/i686-pc-linux-gnu-library/2.13/JGR’

The downloaded packages are in
	‘/tmp/RtmppYO36H/downloaded_packages’
> q ()

Warning messages:
1: In install.packages(pkgs = c("JGR"), lib =
"/home/vikas/R/i686-pc-linux-gnu-library/2.13",  :
  installation of package 'rJava' had non-zero exit status
2: In install.packages(pkgs = c("JGR"), lib =
"/home/vikas/R/i686-pc-linux-gnu-library/2.13",  :
  installation of package 'JavaGD' had non-zero exit status
3: In install.packages(pkgs = c("JGR"), lib =
"/home/vikas/R/i686-pc-linux-gnu-library/2.13",  :
  installation of package 'iplots' had non-zero exit status
4: In install.packages(pkgs = c("JGR"), lib =
"/home/vikas/R/i686-pc-linux-gnu-library/2.13",  :
  installation of package 'JGR' had non-zero exit status

What should I do?  Seems something wrong with JNI!  I am
non-programmer and don't have any idea of what it means.

For wider adoption of open source among my clients, R with a GUI is
very important component.  Any help in making JGR/Deducer work is
highly appreciated.

Thanks
Vikas Garud