I've seen a few posts related to this...but all the suggested solutions ive seen dont seem to work....I am running R in an EC2 instance and ran the following commands to try and install rJava but to no avail...any help would be greatly appreciated.
> install.packages("rJava")
Installing package(s) into ‘/home/ubuntu/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.stat.nus.edu.sg/src/contrib/rJava_0.9-3.tar.gz'
Content type 'application/x-gzip' length 537153 bytes (524 Kb)
opened URL
==================================================
downloaded 524 Kb
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
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 : ''
compiler : ''
header prep.: ''
cpp flags : ''
java libs : '-L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk-amd64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/x86_64-linux-gnu/jni -L/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
configure: error: Java Development Kit (JDK) is missing or not registered in R
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/ubuntu/R/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpaEiskU/downloaded_packages’
> system("sudo R CMD javareconf")
Java interpreter : /usr/bin/java
Java version : 1.6.0_24
Java home path : /usr/lib/jvm/java-6-openjdk-amd64/jre
Java compiler : not present
Java headers gen.:
Java archive tool:
Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib/x86_64-linux-gnu/jni:/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu:/usr/lib/jni:/lib:/usr/lib
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/x86_64-linux-gnu/jni -L/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/jni -L/lib -L/usr/lib -ljvm
JNI cpp flags :
Updating Java configuration in /etc/R
Done.
> install.packages("rJava")
[same as before, just skipping to the error parts...]
java libs : '-L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk-amd64/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib/x86_64-linux-gnu/jni -L/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -L/usr/lib/jni -L/lib -L/usr/lib -ljvm'
configure: error: Java Development Kit (JDK) is missing or not registered in R
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/ubuntu/R/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpaEiskU/downloaded_packages’
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C
[5] LC_MONETARY=C LC_MESSAGES=C LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_2.15.1
The easiest way to get rJava on Ubuntu is to install it from the repositories instead of trying to install it directly from CRAN. From the command line this should do the trick
sudo apt-get install r-cran-rjava
I'm facing the same problem at the moment but the solution doesn't seem to work anymore. Running
sudo apt-get install r-cran-rjava
gives me
The following packages have unmet dependencies:
r-cran-rjava : Depends: r-api-3.4
I'm on Linux Mint Tessa 19.1 und I'm using R version 3.6.1 (2019-07-05)
I had
The following packages have unmet dependencies:
r-cran-rjava : Depends: r-api-3.4
I solved with
sudo apt-get update
sudo apt-get install default-jre
sudo apt-get install default-jdk
and
sudo apt-get install r-cran-rjava
This is worked for me (Linux Mint "Ulyana")
in terminal:
sudo -i
R CMD javareconf
then in RStudio:
install.packages("rJava", dependencies = TRUE)
sudo apt-get install r-cran-rjava
didn't work in R Studio, so I had to use the terminal but then worked perfectly for me.
Related
I have the very common problem that rJava does not install correctly on Ubuntu.
This problem has been dsicussed in multiple places here, here, here, to name a few.
The basic problem is that on installing the rJava package, the following error message is produced
configure: error: Unable to run a simple JNI program. Make sure you have configured R with Java support (see R documentation) and check config.log for failure reason.
Warning in system(cmd) : error in running command
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/jonno/R/x86_64-pc-linux-gnu-library/3.6/rJava’
There are various closely related solutions to this problem. Most of them use sudo R CMD javareconf to configure Java for R (also a -e variant). Some suggest setting the JAVA_HOME path in the environment variables (others say not to). Others suggest uninstalling and re-installing R whilst others suggest installing rJava from cran. There are several who reccomend update alternatives. There are other variants of these solutions.
I have tried combinations of all of the above, and have got nowhere, so am clearly doing something wrong.
entering echo $JAVA_HOME returns
/usr/lib/jvm/java-11-openjdk-amd64
my etc/environment looks like this
PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/$
MKL_THREADING_LAYER=GNU
JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64"
When I run R CMD javaconf, it looks like this
Java interpreter : /usr/lib/jvm/java-11-openjdk-amd64/java
Java version : 11.0.4
Java home path : /usr/lib/jvm/java-11-openjdk-amd64
Java compiler : /usr/lib/jvm/java-11-openjdk-amd64/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/lib/jvm/java-11-openjdk-amd64/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/server -ljvm
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-11-openjdk-amd64/lib/server -ljvm -L/usr/lib/R/lib -lR
JAVA_HOME : /usr/lib/jvm/java-11-openjdk-amd64
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /usr/lib/R
Done.
What am I doing wrong and how do I get rJava to install properly?
EDIT:
having managed to successfully install rJava using sudo apt-get install r-cran-rjava I know get the following error
Error: package or namespace load failed for ‘rJava’:
.onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/usr/lib/R/site-library/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
I've investigated with the original poster (we work at the same place) and the problem is that in OpenJDK11 they moved around some of the .so files that the JVM lives in, specifically libjvm.so which in the Ubuntu package is now in /usr/lib/jvm/java-1.11.0-openjdk-amd64/lib/server/.
This means that even if you install the Ubuntu package for rJava with apt install r-cran-rjava it fails when you try to library(rJava).
The solution is to add /usr/lib/jvm/java-1.11.0-openjdk-amd64/lib/server/ to your $LD_LIBRARY_PATH by adding:
export LD_LIBRARY_PATH=/usr/lib/jvm/java-1.11.0-openjdk-amd64/lib/server:$LD_LIBRARY_PATH
to the end of your ~/.bashrc and starting a new shell (or source ~/.bashrc).
This is something we had to fix for our central installs of OpenJDK e.g. here: https://github.com/UCL-RITS/rcps-buildscripts/blob/master/adoptopenjdk-11.0.3_install.sh#L46
If you want to make this work with Rstudio launched from Gnome, you need to add that directory to ldconfig.
As root (or with sudo) create a file in /etc/ld.so.conf.d/ which you should call something with a .conf extension e.g. java.conf which contains the line:
/usr/lib/jvm/java-1.11.0-openjdk-amd64/lib/server
And then as root run
ldconfig -v
This should add the directory to the locations that executables launched through GNOME search for. This particular part of the problem (GNOME ignoring settings in bashrc) has been a problem in Ubuntu since at least 9.04 (https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/366728/).
I want to install Fselector package in which RWeka is needed but on installing RWeka it throughs me following error:
Error : .onLoad failed in loadNamespace() for 'RWeka', details:
call: .jcall("java/lang/System", "V", "setOut", out)
error: method setOut with signature (Ljava/io/PrintStream;)V not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/gaurav/R/x86_64-pc-linux-gnu-library/3.3/RWeka’
Warning in install.packages :
installation of package ‘RWeka’ had non-zero exit status
ERROR: dependency ‘RWeka’ is not available for package ‘FSelector’
* removing ‘/home/gaurav/R/x86_64-pc-linux-gnu-library/3.3/FSelector’
Warning in install.packages :
installation of package ‘FSelector’ had non-zero exit status
I searched about the same and did some modification with jdk, updated the path to jdk/bin in bashrc, but nothing worked.
Session Info
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
locale:
[1] LC_CTYPE=en_IN.UTF-8 LC_NUMERIC=C LC_TIME=en_IN.UTF-8
[4] LC_COLLATE=en_IN.UTF-8 LC_MONETARY=en_IN.UTF-8 LC_MESSAGES=en_IN.UTF-8
[7] LC_PAPER=en_IN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_0.12.12 digest_0.6.12 mime_0.5 grid_3.3.3 plyr_1.8.4
[6] R6_2.2.2 xtable_1.8-2 gtable_0.2.0 scales_0.4.1 ggplot2_2.2.1
[11] rlang_0.1.1 lazyeval_0.2.0 brew_1.0-6 tools_3.3.3 munsell_0.4.3
[16] Rook_1.1-1 shiny_1.0.4 httpuv_1.3.5 colorspace_1.3-2 htmltools_0.3.6
[21] tibble_1.3.3
Can anyone help me in this.
Thanks in advance
Update 1:#Nanov, I followed the steps but still i received same error, I have openjdk 8 and updated the path in bashrc, & when I used "sudo R CMD javareconf" I get below information:
gaurav#gaurav-ds:~$ sudo R CMD javareconf
Java interpreter : /usr/lib/jvm/java-8-oracle/jre/bin/java
Java version : 1.8.0_131
Java home path : /usr/lib/jvm/java-8-oracle/jre
Java compiler : not present
Java headers gen.:
Java archive tool:
trying to compile and link a JNI program
detected JNI cpp flags :
detected JNI linker flags : -L/usr/lib -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time-D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.oconftest.c:1:17: fatal error: jni.h: No such file or directory
#include <jni.h>
^
compilation terminated.
/usr/lib/R/etc/Makeconf:132: recipe for target 'conftest.o' failed
make: *** [conftest.o] Error 1
Unable to compile a JNI program.
JAVA_HOME : /usr/lib/jvm/java-8-oracle/jre
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.
sudo apt-get install r-cran-rjava
sudo apt-get install openjdk-8-jdk
sudo rm -rf /usr/lib/jvm/default-java
sudo ln -s /usr/lib/jvm/java-8-openjdk-amd64/ /usr/lib/jvm/default-java
sudo R CMD javareconf
sudo R
install.packages(“RWeka”)
Better install openjdk-8-jdk, because in the newest version -9- is bug.
I was trying to install the xlsx package, unfortunately, there is an issue with Java, which I am unable to solve.
Please find below the output produced when trying to install the package xlsx.
Here's the output:
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 is installed:
java -version gives the following output:
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" leads to:
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.
Nonetheless, install.packages('rJava') leads to:
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 have no idea how to fix this java problem. I work with RStudio and Fedora.
Your help is much appreciated.
Thanks
Tamas
If you have Java installed, try resetting R's java configuration from the commandline
sudo R CMD javareconf
Then try again to install just rJava (you might restart RStudio first)
install.packages('rJava')
If this still didn't solve your problem, the error shows that R could not load getsp.:
checking whether Java run-time works...
Error: Could not find or load main class getsp
First verify that getsp is accessible.
locate getsp
The output may contain several items but you should find something like this:
/usr/share/R/share/java/getsp.class
Then we want this to be accessible so export it so 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 rest would be JAVA_HOME and rerun the 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
It is also recommended to unset CLASSPATH in the rJava issues as it may cause other issues down the line. You probably should do this before trying to change JAVA_HOME and reset again if this still doesn't solve the problem.
EDIT
Given that this question has remained 'unanswered' for quite some time I thought I should also add my recommendation to just use the readxl package instead which does not use Java. It installs much easier and is part of the tidyverse. Just a general recommendation for those trying to work with excel files.
Okay, I finally managed it by adding "JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.25.x86_64/jre/" to .bashrc in my home folder.
Thank you for your help, cdeterman.
Best Tamas
It is the problem of Java. I think that you have not installed Java on your system. Check if Java already installed:
java -version
If it returns "The program java can be found in the following packages", Java hasn't been installed yet, so execute the following command:
sudo apt-get install default-jre
sudo apt-get install default-jdk
Then try to reinstall the package.
This solution worked for me perfectly:
https://orajavasolutions.wordpress.com/2014/06/03/installing-and-loading-xlsx-package-in-r-with-ubuntu/
I am not able to call rJava package in R 3.0. I got the following message
Error: package ‘rJava’ was built before R 3.0.0: please re-install it
I am getting error when I tried to re-install rJava package. I have provided the output of R CMD javareconf
Java interpreter : /usr/bin/java
Java version : 1.7.0_21
Java home path : /usr/lib/jvm/java-7-openjdk-i386/jre
Java compiler : /usr/lib/jvm/java-7-openjdk-i386/jre/../bin/javac
Java headers gen.: /usr/lib/jvm/java-7-openjdk-i386/jre/../bin/javah
Java archive tool: /usr/lib/jvm/java-7-openjdk-i386/jre/../bin/jar
trying to compile and link a JNI progam
detected JNI cpp flags :
detected JNI linker flags :
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O2 -pipe -g -c conftest.c -o conftest.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
compilation terminated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.
I am using Ubuntu 13.04. I also tried apt-get install r-cran-rjava which is not helping to solve the issue. Regarding jni.h there were some solution here. But, not sure how can I use the solution here.
I ran into the exact same issue. My solution was to install the openjdk-7-* via
sudo apt-get install openjdk-7-*
Followed that with
sudo R CMD javareconf
and I was then able to install rJava in R via install.packages("rJava").
While perhaps not the most elegant solution it appears to have solved my problems with getting rJava to work.
For those getting the error:
error: unable to load shared object '/some/dir/rJava/libs/rJava.so': libjvm.so:
cannot open shared object file: No such file or directory
I solved the error locating the library in the system and linking them to /usr/lib:
$sudo updatedb
$locate libjvm.so
/usr/lib/debug/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server/libjvm.so
/usr/lib/debug/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/zero/libjvm.so
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/jamvm/libjvm.so
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server/libjvm.so
/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/zero/libjvm.so
$sudo ln -s /usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server/libjvm.so /usr/lib/
Installing rJava from the distribution packages as proposed in this askUbuntu answer also works:
sudo apt-get install r-cran-rjava
NOTE: tried from a Debian system.
I was also facing same error which was on RHEL8.1 & i resolved it as follows:
yum --enablerepo=* install java-1.8*
later i ran same command which was giving me error logs of R server.
R CMD javareconf
which turns into following output.
When I tried to run the R console in Eclipse, I got this error:
....Please make sure that R package 'rj' (1.1 or compatible) is installed...
So I tried to install it in the R console like this:
install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-1.1")
and got this error:
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'rj.gd', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/alex/R/x86_64-pc-linux-gnu-library/2.15/rj.gd/libs/rj.gd.so':
libjvm.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
and I found that when installing rJava using: install.packages("rJava") gets a similar error:
** testing if installed package can be loaded
Error : .onLoad failed in loadNamespace() for 'rJava', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/alex/R/x86_64-pc-linux-gnu-library/2.15/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
When I run sudo R CMD javareconf,I got this output:
Java interpreter : /usr/bin/java
Java version : 1.7.0
Java home path : /usr/lib/jvm/java-7-oracle/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
NOTE: Your JVM has a bogus java.library.path system property!
Trying a heuristic via sun.boot.library.path to find jvm library...
Java library path: $(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/lib/amd64/server
JNI linker flags : -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/lib/amd64/server -ljvm
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
Updating Java configuration in /etc/R
Done.
by the way,my configuration is:
Ubuntu 11.10 64bit
Eclipse 3.7
Oracle-1.7-jdk
R version 2.15.1
For Linux(Ubuntu) users: If you have oracle-java (7/8) installed. It'll be at this location /usr/lib/jvm and sudo access is required.
Create the file /etc/ld.so.conf.d/java.conf with the following entries:
/usr/lib/jvm/java-8-oracle/jre/lib/amd64
/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server
(Replace java-8-oracle with java-7-oracle depending on your java version)
Then:
sudo ldconfig
Restart RStudio and then install the rJava package.
OR
Also an alternative method is to export LD_LIBRARY_PATH with the value of Java library path obtained from the command R CMD javareconf -e and run install.packages
I got similar issue and was able to resolve it by running
R CMD javareconf -e
Output of the R CMD javareconf -e
Java interpreter : /export/apps/jdk/JDK-1_6_0_27/jre/bin/java
Java version : 1.6.0_27
Java home path : /export/apps/jdk/JDK-1_6_0_27
Java compiler : /export/apps/jdk/JDK-1_6_0_27/bin/javac
Java headers gen.: /export/apps/jdk/JDK-1_6_0_27/bin/javah
Java archive tool: /export/apps/jdk/JDK-1_6_0_27/bin/jar
Java library path: /export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64/server:/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64:/export/apps/jdk/JDK-1_6_0_27/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
JNI linker flags : -L/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64/server -L/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64 -L/export/apps/jdk/JDK-1_6_0_27/jre/../lib/amd64 -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm
JNI cpp flags : -I/export/apps/jdk/JDK-1_6_0_27/include -I/export/apps/jdk/JDK-1_6_0_27/include/linux
The following Java variables have been exported:
JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH
Running: /bin/bash
After setting LD_LIBRARY_PATH to the same value as JAVA_LD_LIBRARY_PATH as shown in the output above. I was able to install rj.
export LD_LIBRARY_PATH=/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64/server:/export/apps/jdk/JDK-1_6_0_27/jre/lib/amd64:/export/apps/jdk/JDK-1_6_0_27/jre/../lib/amd64:/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib
Run R and then install rj by
install.packages(c("rj", "rj.gd"), repos="http://download.walware.de/rj-1.1")
I found the solution:
export LD_LIBRARY_PATH=/usr/lib/jvm/java-7-oracle/lib/amd64:/usr/lib/jvm/java-7-oracle/jre/lib/amd64/server
then
sudo R CMD javareconf
Note: The path (java-7-oracle) needs to be updated based on your Java installation.
I did the following and it worked for me:
export LD_LIBRARY_PATH=$JAVA_LD_LIBRARY_PATH
sudo R CMD javareconf
I had to restart R then as well.
Years later, I ended up on this question after searching for an error reported by R after I had unsuccessfully installed a package on that required shifting to Oracle's Java.
All I had to do to fix it was:
$ sudo R CMD javareconf
or just set the library in R?
I just ran this command in R:
Sys.setenv(JAVA_HOME='/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server')
(replace "/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server" with your Java library path which can be found running "sudo R CMD javareconf")
Might not be the most elegant solution - but it worked for me!
I did not had the jdk installed which I could fix with
sudo apt-get install jdk-*
After that i could run the sudo R CMD javareconf which always drew an error message before. Everything was set correctly and no manual tweeks where required, and after that package installation ran smootly in R (restart required).
When facing missing limjvm.so errors make sure that the correct ldpaths is picked up from the standard configuration in /etc/R versus the one in /usr/lib/R/etc.
This fixes the LD_LIBRARY_PATH problem for me (Linux, Debian 7.1.0, tc-shell, R version 3.0.2):
Add this line to .cshrc:
setenv LD_LIBRARY_PATH $JAVA_HOME/jre/lib/amd64:$JAVA_HOME/jre/lib/amd64/server
Adding this command to ~/.login was not enough; the environment variable LD_LIBRARY_PATH was still not known in new xterms: echo $LD_LIBRARY_PATH : LD_LIBRARY_PATH: Undefined variable. (Why??)
Curiously, when starting R as superuser, there was no problem with finding libjvm.so .
I fixed this by just running R with sudo, and then running install.packages('rJava`).
None of the above worked for me, the only solution that installed rJava on Linux Ubuntu without any problems was to pass RScript command after installation of the base R:
$ sudo Rscript -e 'install.packages("rJava", repos = "http://cran.r-project.org/")'