Geek Answers Handbook

R-Project: xlsx package installation error (due to Java issues)

I tried to install the xlsx package, unfortunately there is a problem with Java that I cannot solve.

The following is the result obtained when trying to install the xlsx package.

Here's the conclusion:

R version 3.1.1 (2014-07-10) -- "Sock it to Me" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-redhat-linux-gnu (64-bit) 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("xlsx") Installing package into '/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1' (as 'lib' is unspecified) also installing the dependencies 'rJava', 'xlsxjars' trying URL 'contrib/rJava_0.9-6.tar.gz' Content type 'application/x-gzip' length 567515 bytes (554 Kb) opened URL ================================================== downloaded 554 Kb trying URL 'contrib/xlsxjars_0.6.1.tar.gz' Content type 'application/x-gzip' length 9477071 bytes (9.0 Mb) opened URL ================================================== downloaded 9.0 Mb trying URL 'contrib/xlsx_0.5.7.tar.gz' Content type 'application/x-gzip' length 312839 bytes (305 Kb) opened URL ================================================== downloaded 305 Kb * installing *source* package 'rJava' ... ** package 'rJava' successfully unpacked and MD5 sums checked checking for gcc... gcc -m64 -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 -m64 -std=gnu99 accepts -g... yes checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -m64 -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 -m64 -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 : '/bin/java' archiver : '/bin/jar' compiler : '/bin/javac' header prep.: '/bin/javah' cpp flags : '-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include/linux' java libs : '-L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/lib/amd64/server -ljvm' checking whether Java run-time works... Error: Could not find or load main class getsp no configure: error: Java interpreter '/bin/java' does not work ERROR: configuration failed for package 'rJava' * removing '/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1/rJava' Warning in install.packages : installation of package 'rJava' had non-zero exit status ERROR: dependency 'rJava' is not available for package 'xlsxjars' * removing '/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1/xlsxjars' Warning in install.packages : installation of package 'xlsxjars' had non-zero exit status ERROR: dependencies 'rJava', 'xlsxjars' are not available for package 'xlsx' * removing '/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1/xlsx' Warning in install.packages : installation of package 'xlsx' had non-zero exit status The downloaded source packages are in '/tmp/Rtmpj1UG8a/downloaded_packages'

Java installed:

java -version gives the following result:

 java version "1.7.0_71" OpenJDK Runtime Environment (fedora-2.5.3.0.fc20-x86_64 u71-b14) OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)

"sudo R CMD javareconf" results in:

 Java interpreter : /bin/java Java version : 1.7.0_71 Java home path : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre Java compiler : /bin/javac Java headers gen.: /bin/javah Java archive tool: /bin/jar trying to compile and link a JNI progam 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 -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include/linux -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c conftest.c -o conftest.o gcc -m64 -std=gnu99 -shared -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/lib/amd64/server -ljvm -L/usr/lib64/R/lib -lR JAVA_HOME : /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/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.

However, install.packages ('rJava') results in:

 checking Java support in R... present: interpreter : '/bin/java' archiver : '/bin/jar' compiler : '/bin/javac' header prep.: '/bin/javah' cpp flags : '-I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include -I/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/../include/linux' java libs : '-L/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71-2.5.3.0.fc20.x86_64/jre/lib/amd64/server -ljvm' checking whether Java run-time works... Error: Could not find or load main class getsp no configure: error: Java interpreter '/bin/java' does not work ERROR: configuration failed for package 'rJava' * removing '/home/tamaspavlicek/R/x86_64-redhat-linux-gnu-library/3.1/rJava' Warning in install.packages : installation of package 'rJava' had non-zero exit status The downloaded source packages are in '/tmp/Rtmpnl17m7/downloaded_packages'

I do not know how to fix this java problem. I work with RStudio and Fedora. Your help is greatly appreciated.

thanks

Tamash

+7
java r xlsx rjava
source share
4 answers

If you have Java installed, try resetting the java R configuration from the command line

 sudo R CMD javareconf

Then try to install only rJava

 install.packages('rJava')

If this still does not solve your problem, the error indicates that R could not load getp .:

 checking whether Java run-time works... Error: Could not find or load main class getsp

First make sure getp is available.

 locate getsp

The output may contain several elements, but you should find something like this:

 /usr/share/R/share/java/getsp.class

Then we want it to be available, so export it so that R can find it:

 export CLASSPATH=/usr/share/R/share/java

In the same window, start another R session and try installing rJava again.

Another thing to relax is JAVA_HOME and restart javareconf

 export JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre export PATH=$PATH:$JAVA_HOME/bin sudo R CMD javareconf

Unset unset CLASSPATH in rJava problems is also recommended, as this may cause other problems. You should probably do this before trying to change JAVA_HOME and reset again if this has not solved the problem.

+10
source share

Well, I managed to do this by adding "JAVA_HOME = / usr / lib / jvm / java-1.8.0-openjdk-1.8.0.25.x86_64 / jre /" to my home folder. Bashrc.

Thank you for your help, cdeterman.

Best tamas

+1
source share

This is a Java issue. I think you did not install Java on your system. Check if Java has already been installed:

 java -version

If it returns "The java program can be found in the following packages", Java is not installed yet, so run the following command:

 sudo apt-get install default-jre sudo apt-get install default-jdk

Then try reinstalling the package.

0
source share

This solution works fine for me:

 https://orajavasolutions.wordpress.com/2014/06/03/installing-and-loading-xlsx-package-in-r-with-ubuntu/
-one
source share

More articles:


All Articles