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Thread: Installing packages in R: "Java configuration variables are not set"

  1. #1

    Default Installing packages in R: "Java configuration variables are not set"

    Dear users,
    When trying to install packages in R, I get the following error. Would be great if you could help me out here.

    " 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."


    I think it has something to do with the compiler, but I am not sure. When running R CMD javareconf in root mode, I get the following information. Any suggestions on how to fix this?

    "R CMD javareconf
    Java interpreter : /usr/lib64/jvm/java/jre/bin/java
    Java version : 1.5.0
    Java home path : /usr/lib64/jvm/java
    /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o: In function `_start':
    /home/abuild/rpmbuild/BUILD/glibc-2.18/csu/../sysdeps/x86_64/start.S:118: undefined reference to `main'
    collect2: error: ld returned 1 exit status
    Java compiler : not functional
    Java headers gen.: /usr/lib64/jvm/java/bin/javah
    Java archive tool: /usr/lib64/jvm/java/bin/jar

    trying to compile and link a JNI progam
    detected JNI cpp flags :
    detected JNI linker flags : -L/usr/lib64/../lib64/gcj-4.8-14 -ljvm
    gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -c conftest.c -o conftest.o
    gcc -std=gnu99 -shared -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib64/../lib64/gcj-4.8-14 -ljvm -L/usr/lib64/R/lib -lR

    JAVA_HOME : /usr/lib64/jvm/java
    Java library path: /usr/lib64/../lib64/gcj-4.8-14
    JNI cpp flags :
    JNI linker flags : -L/usr/lib64/../lib64/gcj-4.8-14 -ljvm
    Updating Java configuration in /usr/lib64/R"

    Many thanks in advance!!

  2. #2
    Join Date
    Jun 2008
    Location
    Netherlands
    Posts
    29,798

    Default Re: Installing packages in R: "Java configuration variables are not set"

    Hello and welcome here.

    Please alwyas tell which version of openSUSE you use.

    Also, when you post computer text here in a post (copied/pasted from a terminal window), do so between CODE tags. You get them by clicking on the # button in the tooll bar of the post editor.

    And when you do something like "When trying to install packages in R". do not tell the story alone, but show what you are exectly doing. Do not think that there is obvious only one way to do things and that thus everybody knows what you are doing. Often there are more ways to achieve the same and we can not guess what you do. Also when "trying", you could make errors, but we can not see them when you do not show what you do.
    Henk van Velden

  3. #3

    Default Re: Installing packages in R: "Java configuration variables are not set"

    Sorry for the confusion, thanks for the suggestions,

    I am using SUSE 13.1. When trying to install packages in R - Konsole (
    Code:
    install.packages("XLConnect")
    , I get the following error.

    Code:
     * installing *source* package ‘rJava’ ...
    ** package ‘rJava’ successfully unpacked and MD5 sums checked
    configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
    checking for gcc... gcc -std=gnu99
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables... 
    checking whether we are cross compiling... no
    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/lib64/jvm/java/jre/bin/java'
    archiver    : '/usr/lib64/jvm/java/bin/jar'
    compiler    : '/usr/lib64/jvm/java/bin/javac'
    header prep.: '/usr/lib64/jvm/java/bin/javah'
    cpp flags   : ''
    java libs   : '-L/usr/lib64/../lib64/gcj-4.8-14 -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 ‘/home/remco/R/x86_64-suse-linux-gnu-library/3.0/rJava’
    ERROR: dependency ‘rJava’ is not available for package ‘XLConnect’
    * removing ‘/home/remco/R/x86_64-suse-linux-gnu-library/3.0/XLConnect’
    
    The downloaded source packages are in
            ‘/tmp/Rtmpe5yoq8/downloaded_packages’
    Warning messages:
    1: In install.packages("XLConnect") :
      installation of package ‘rJava’ had non-zero exit status
    2: In install.packages("XLConnect") :
      installation of package ‘XLConnect’ had non-zero exit status
    I think it has something to do with the compiler, but I am not sure. When running
    Code:
    R CMD javareconf
    in Terminal root mode, I get the following information. Any suggestions on how to fix this?

    Code:
    R CMD javareconf
    Java interpreter : /usr/lib64/jvm/java/jre/bin/java
    Java version     : 1.5.0
    Java home path   : /usr/lib64/jvm/java
    /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64/crt1.o: In function `_start':
    /home/abuild/rpmbuild/BUILD/glibc-2.18/csu/../sysdeps/x86_64/start.S:118: undefined reference to `main'
    collect2: error: ld returned 1 exit status
    Java compiler    : not functional
    Java headers gen.: /usr/lib64/jvm/java/bin/javah
    Java archive tool: /usr/lib64/jvm/java/bin/jar
    
    trying to compile and link a JNI progam 
    detected JNI cpp flags    : 
    detected JNI linker flags : -L/usr/lib64/../lib64/gcj-4.8-14 -ljvm
    gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG  -I/usr/local/include     -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall  -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables  -fasynchronous-unwind-tables -g  -c conftest.c -o conftest.o
    gcc -std=gnu99 -shared -L/usr/local/lib64 -o conftest.so conftest.o  -L/usr/lib64/../lib64/gcj-4.8-14 -ljvm -L/usr/lib64/R/lib -lR
    
    JAVA_HOME        : /usr/lib64/jvm/java
    Java library path: /usr/lib64/../lib64/gcj-4.8-14
    JNI cpp flags    : 
    JNI linker flags : -L/usr/lib64/../lib64/gcj-4.8-14 -ljvm
    Updating Java configuration in /usr/lib64/R
    
    

  4. #4

    Default Re: Installing packages in R: "Java configuration variables are not set"

    When trying to install another package through the R - Konsole I get:

    Code:
    > 
    install.packages("plyr")
    Installing package into ‘/home/remco/R/x86_64-suse-linux-gnu-library/3.0’
    (as ‘lib’ is unspecified)
    also installing the dependency ‘Rcpp’
    
    trying URL 'http://cran-mirror.cs.uu.nl/src/contrib/Rcpp_0.11.1.tar.gz'
    Content type 'application/x-gzip' length 2003515 bytes (1.9 Mb)
    opened URL
    ==================================================
    downloaded 1.9 Mb
    
    trying URL 'http://cran-mirror.cs.uu.nl/src/contrib/plyr_1.8.1.tar.gz'
    Content type 'application/x-gzip' length 393233 bytes (384 Kb)
    opened URL
    ==================================================
    downloaded 384 Kb
    
    * installing *source* package ‘Rcpp’ ...
    ** package ‘Rcpp’ successfully unpacked and MD5 sums checked
    ** libs
    Warning: R include directory is empty -- perhaps need to install R-devel.rpm or similar
    g++ -I/usr/lib64/R/include -DNDEBUG -I../inst/include/ -I/usr/local/include    -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g  -c Date.cpp -o Date.o
    In file included from ../inst/include/Rcpp.h:27:0,
                     from Date.cpp:31:
    ../inst/include/RcppCommon.h:36:15: fatal error: R.h: No such file or directory
     #include <R.h>
                   ^
    compilation terminated.
    make: *** [Date.o] Error 1
    ERROR: compilation failed for package ‘Rcpp’
    * removing ‘/home/remco/R/x86_64-suse-linux-gnu-library/3.0/Rcpp’
    ERROR: dependency ‘Rcpp’ is not available for package ‘plyr’
    * removing ‘/home/remco/R/x86_64-suse-linux-gnu-library/3.0/plyr’
    
    The downloaded source packages are in
            ‘/tmp/Rtmpe5yoq8/downloaded_packages’
    Warning messages:
    1: In install.packages("plyr") :
      installation of package ‘Rcpp’ had non-zero exit status
    2: In install.packages("plyr") :
      installation of package ‘plyr’ had non-zero exit status

  5. #5
    Join Date
    Feb 2010
    Location
    Germany
    Posts
    4,654

    Default Re: Installing packages in R: "Java configuration variables are notset"

    Most likely you need to install the package java-1_7_0-openjdk-devel first.

    --
    PC: oS 13.1 x86_64 | i7-2600@3.40GHz | 16GB | KDE 4.11 | GTX 650 Ti
    ThinkPad E320: oS 13.1 x86_64 | i3@2.30GHz | 8GB | KDE 4.11 | HD 3000
    HTPC: oS 13.1 x86_64 | Celeron@1.8GHz | 2GB | Gnome 3.10 | HD 2500

  6. #6
    Join Date
    Feb 2010
    Location
    Germany
    Posts
    4,654

    Default Re: Installing packages in R: "Java configuration variables are notset"

    Am 09.05.2014 19:56, schrieb Molenhuis:
    > ../inst/include/RcppCommon.h:36:15: fatal error: R.h: No such file or directory


    Of course you need to install R-base-devel with yast or zypper before
    you can use the R package system as it often will compile some software
    from the downloaded source archives.

    --
    PC: oS 13.1 x86_64 | i7-2600@3.40GHz | 16GB | KDE 4.11 | GTX 650 Ti
    ThinkPad E320: oS 13.1 x86_64 | i3@2.30GHz | 8GB | KDE 4.11 | HD 3000
    HTPC: oS 13.1 x86_64 | Celeron@1.8GHz | 2GB | Gnome 3.10 | HD 2500

  7. #7

    Default Re: Installing packages in R: "Java configuration variables are not set"

    Thanks a lot! The plyr package is now working. The XLConnect package still gave the same problem, I managed to get the job done by using a different package to import excel files.

  8. #8
    Join Date
    Mar 2014
    Location
    Dnepropetrovsk
    Posts
    105

    Default Re: Installing packages in R: "Java configuration variables are not set"

    I had the same problem on openSUSE 42.1 when installing rJava package.

    In R:
    Code:
    > install.packages("rJava")
    . . .
    checking Java support in R... present:
    interpreter : '/usr/lib64/jvm/jre/bin/java'
    archiver    : '/usr/lib64/jvm/jre/../bin/jar'
    compiler    : '/usr/lib64/jvm/jre/../bin/javac'
    header prep.: '/usr/lib64/jvm/jre/../bin/javah'
    cpp flags   : ''
    java libs   : '-L/usr/lib64/jvm/jre/lib/amd64/server -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/lib64/R/library/rJava’
    
    The downloaded source packages are in
            ‘/tmp/RtmpLZqJ3r/downloaded_packages’
    Updating HTML index of packages in '.Library'
    Making 'packages.html' ... done
    Warning message:
    In install.packages("rJava") :
      installation of package ‘rJava’ had non-zero exit status
    In console as root:
    Code:
    # R CMD javareconf
    Java interpreter : /usr/lib64/jvm/jre/bin/java
    Java version     : 1.8.0_101
    Java home path   : /usr/lib64/jvm/jre
    Java compiler    : /usr/lib64/jvm/jre/../bin/javac
    Java headers gen.: /usr/lib64/jvm/jre/../bin/javah
    Java archive tool: /usr/lib64/jvm/jre/../bin/jar
    
    trying to compile and link a JNI program 
    detected JNI cpp flags    : 
    detected JNI linker flags : -L/usr/lib64/jvm/jre/lib/amd64/server -ljvm
    gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g  -c conftest.c -o conftest.o
    gcc -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib64/jvm/jre/lib/amd64/server -ljvm -L/usr/lib64/R/lib -lR
    
    
    JAVA_HOME        : /usr/lib64/jvm/jre
    Java library path: /usr/lib64/jvm/jre/lib/amd64/server
    JNI cpp flags    : 
    JNI linker flags : -L/usr/lib64/jvm/jre/lib/amd64/server -ljvm
    Updating Java configuration in /usr/lib64/R
    Done.
    I followed this post:
    Code:
    # unset JAVA_HOME
    # R CMD javareconf
    Java interpreter : /usr/bin/java
    Java version     : 1.8.0_101
    Java home path   : /usr/lib64/jvm/java-1.8.0-openjdk-1.8.0/jre
    Java compiler    : /usr/bin/javac
    Java headers gen.: /usr/bin/javah
    Java archive tool: /usr/bin/jar
    
    trying to compile and link a JNI program 
    detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
    detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
    gcc -std=gnu99 -I/usr/lib64/R/include -DNDEBUG -I/usr/lib64/jvm/java-1.8.0-openjdk-1.8.0/jre/../include -I/usr/lib64/jvm/java-1.8.0-openjdk-1.8.0/jre/../include/linux -I/usr/local/include    -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g  -c conftest.c -o conftest.o
    gcc -std=gnu99 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o conftest.so conftest.o -L/usr/lib64/jvm/java-1.8.0-openjdk-1.8.0/jre/lib/amd64/server -ljvm -L/usr/lib64/R/lib -lR
    
    
    JAVA_HOME        : /usr/lib64/jvm/java-1.8.0-openjdk-1.8.0/jre
    Java library path: $(JAVA_HOME)/lib/amd64/server
    JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
    JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
    Updating Java configuration in /usr/lib64/R
    Done.
    Then rJava has been installed successfully.

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