Regarding the error, trying to make sure you have JDK install. This does not solve the problem directly, but it helps to avoid other bugs with Rstudio. JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvmįirst i would recommend installing Rstudio from its website: (i.e. Java library path: $(JAVA_HOME)/lib/amd64/server JAVA_HOME : /usr/lib/jvm/java-7-openjdk-amd64/jre Gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR Gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-7-openjdk-amd64/jre/./include -fpic -g -O2 -fstack-protector -param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o Java home path : /usr/lib/jvm/java-7-openjdk-amd64/jreĭetected JNI cpp flags : -I$(JAVA_HOME)/./includeĭetected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm You should then see something like this: $ sudo R CMD javareconf Make sure you do NOT set JAVA_HOME by hand - it will be detected automatically.
R LIBRARY RJAVA INSTALL
You will need at least sudo apt-get install openjdk-7-jdk In short, I want to be able to use RStudio with rJava again without it destroying any other uses of Java (such as jmol). I've also un-installed and re-installed RStudio via the Ubuntu Software Centre but this didn't make any difference. I tried to follow these links, one and two but they didn't seem to resolve my issue there are more links on SO but I'm not sure which one to follow. Updating Java configuration in /usr/lib/R
Gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector -param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.oĬonftest.c:1:17: fatal error: jni.h: No such file or directory Which also gave the following error, trying to compile and link a JNI programĭetected JNI linker flags : -L/usr/lib/jvm/java-7-openjdk-amd64/jre/lib/amd64/server -ljvm So, I went to the terminal and typed, sudo R CMD javareconf
Installation of package ‘rJava’ had non-zero exit status To set all Java-related variables and then install rJava.ĮRROR: configuration failed for package ‘rJava’
R LIBRARY RJAVA FULL
Make sure R is configured with full Java support (including JDK). Which returned the following error message, configure: error: One or more Java configuration variables are not set. I tried to install it again using, install.packages("rJava")
R LIBRARY RJAVA UPGRADE
I'm using RStudio on and Ubuntu box (14.04) and I tried to upgrade rJava from sources and in the process I managed to lose it. I've tried to solve this using the previous questions/answers on SO but without any success.
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