error: unable to load installed packages just now

问题:

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  

回答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

回答2:

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") 

回答3:

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 

回答4:

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.

回答5:

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

回答6:

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!

回答7:

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.

回答8:

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 .

回答9:

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).

回答10:

I fixed this by just running R with sudo, and then running install.packages('rJava`).

回答11:

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/")' 

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