Re: [R] JGR/Deducer Installation

From: Ista Zahn <izahn_at_psych.rochester.edu>
Date: Thu, 26 May 2011 18:22:37 -0400

Hi Vikas,
I've found it nessessary to do

su
R CMD javareconf

After java updates. Then install/update JGR etc. if desired.

Note that for whatever reason 'sudo R CMD javareconf' doesn't seem to work for me, I have to actually become root with su and then run R CMD javareconf

Best,
Ista

On Thu, May 26, 2011 at 10:35 AM, Vikas Garud <information4vikas_at_gmail.com> wrote:
> 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
>
> ______________________________________________
> R-help_at_r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org

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and provide commented, minimal, self-contained, reproducible code.
Received on Thu 26 May 2011 - 22:29:20 GMT

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