[BioC] error while installing Java related packages

[Martin Morgan]

On 03/16/2011 06:46 AM, Martin Morgan wrote:
> On 03/16/2011 05:01 AM, MLSC MANIPAL wrote:
>> *Dear Sir,
>> I have successfully installed jdk and rJava using the following commands:
>>
>> sudo apt-get install r-cran-rjava
>>
>> sudo apt-get install sun-java6-jdk sun-java6-jre
>>
>> But when I try to install using : install.packages("rJava"), it is giving
>> the follwinfg error:
>> *
>> Warning in install.packages("rJava") :
>> 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
>> trying URL 'http://cran.ma.imperial.ac.uk/src/contrib/rJava_0.8-8.tar.gz'
>> Content type 'application/x-gzip' length 522057 bytes (509 Kb)
>> opened URL
>> ==================================================
>> downloaded 509 Kb
>>
>> * 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... /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
>> 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 : ''
>> java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/i386/server
>> -L/usr/lib/jvm/java-6-openjdk/jre/lib/i386
>> -L/usr/lib/jvm/java-6-openjdk/jre/../lib/i386
>> -L/usr/java/packages/lib/i386
>> -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
>> configure: error: One or more Java configuration variables are not set.
>> Make sure R is configured with full Java support (including JDK). Run
>> R CMD javareconf
>> as root to add Java support to R.
>>
>> If you don't have root privileges, run
>> R CMD javareconf -e
>> to set all Java-related variables and then install rJava.
>>
>> ERROR: configuration failed for package ‘rJava’
>> * removing ‘/usr/local/lib/R/site-library/rJava’
>> * restoring previous ‘/usr/local/lib/R/site-library/rJava’
>>
>> The downloaded packages are in
>> ‘/tmp/Rtmpp8n1WE/downloaded_packages’
>> Warning message:
>> In install.packages("rJava") :
>> installation of package 'rJava' had non-zero exit status
>>
>> *The same problem while installing Java related web packages such as
>> RWebService,Sjava,JavaGD etc...
>> *
>> *I am using R version 2.11.1 (2010-05-31)*
>>
>> *I already run the following command in root and it was successful: R CMD
>> javareconf
>>
>> *Java interpreter : /usr/bin/java
>> Java version : 1.6.0_20
>> Java home path : /usr/lib/jvm/java-6-openjdk/jre
>> Java compiler : /usr/bin/javac
>> Java headers gen.: /usr/bin/javah
>> Java archive tool: /usr/bin/jar
>> Java library path:
>> $(JAVA_HOME)/lib/i386/server:$(JAVA_HOME)/lib/i386:$(JAVA_HOME)/../lib/i386:/usr/java/packages/lib/i386:/usr/lib/jni:/lib:/usr/lib
>>
>> JNI linker flags : -L$(JAVA_HOME)/lib/i386/server -L$(JAVA_HOME)/lib/i386
>> -L$(JAVA_HOME)/../lib/i386 -L/usr/java/packages/lib/i386 -L/usr/lib/jni
>> -L/lib -L/usr/lib -ljvm
>> JNI cpp flags :
>
> Both rJava and SJava have this in their configuration file
>
> if test -n "${JAVA}" && test -n "${JAVAC}" && test -n "${JAVAH}" && \
> test -n "${JAVA_CPPFLAGS}" && test -n "${JAVA_LIBS}" && test -n
> "${JAR}"; then
> have_all_flags=yes;
> fi
>
> so I suspect they fail because JAVA_CPPFLAGS is '' (for me, this has the
> value -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux). It seems
> like R CMD javareconf should be determining this (javareconf is in
> R_HOME/bin/). You might manually edit R_HOME/etc/ so that JAVA_CPPFLAGS

meant R_HOME/etc/Makeconf

> points to something appropriate (the location of the include files
> requires for your java installation).
>
> It might help to install a newer version of R.
>
> Martin
>
>> Updating Java configuration in /etc/R
>> Done.*
>>
>> *
>>
>> *
>> *
>>
>> *Hence, Can you please suggest me a solution for this?*
>>
>> * *
>>
>> *Thanking you in anticipation.*
>>
>> * *
>>
>> *Regards,*
>>
>> *Rayan*
>>
>> [[alternative HTML version deleted]]
>>
>>
>>
>>
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>
>


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