[R] JGR / linux

[g-h-d]

Thanks. 

I basically followed the steps in http://lib.stat.cmu.edu/R/CRAN/, and those
below for JGR and it worked.

...but there are problems with help files e.g. ?matrix generates the
following message:

/tmp/RtmpvxsnQa/.R/doc/html/packages.html (No such file or directory)



g-h-d wrote:
> 
> 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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