[R] JGR / linux

g-h-d erwann.rogard at gmail.com
Tue Jun 3 22:44:23 CEST 2008 



Dirk Eddelbuettel wrote:
> 
> 
> On 3 June 2008 at 08:42, g-h-d wrote:
> | 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)
> 
> I think you can ignore that. It's just a warning.  The rest of your steps
> were very sound.
> 
> In particular ...
> 
> | 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
> 
> ... a very good idea to realign what command will default to being '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
> 
> ... but given that javareconf also looks after javac and javah, I
> recommend
> doing the same update-alternatives call for 'javah' and 'javac'.
> 
> I just re-did that on a Ubuntu 8.04, 32bit, machine and it re-built rJava,
> JGR, JavaGD, ... without a hitch.
> 
> Dirk
> 
> 
> | > 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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> | 
> | ______________________________________________
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> | https://stat.ethz.ch/mailman/listinfo/r-help
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> | and provide commented, minimal, self-contained, reproducible code.
> 
> -- 
> Three out of two people have difficulties with fractions.
> 
> ______________________________________________
> 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.
> 
> 

About the message resulting from calling say ?matrix: the message may be a
warning, but ?matrix just doesnt work, I can't use it (or any other help
command).

About "doing the same update-alternatives call for 'javah' and 'javac'." I
actually don't know what you mean exactly. Could you please clarify? Thanks.



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