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sudo R CMD javareconf solution not working

I am trying to run rJava in RStudio but without success:
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 '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava/libs/rJava.so
Reason: image not found
Using the common solution for rJava issues, 'sudo R CMD javareconf' doesn't work and gives me this ouput:
Java interpreter : /usr/bin/java
Java version : 11.0.6
Java home path : /Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home
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/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c conftest.c -o conftest.o
clang-7: warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk' [-Wmissing-sysroot]
In file included from conftest.c:1:
/Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home/include/jni.h:39:10: fatal error:
'stdio.h' file not found
#include <stdio.h>
^~~~~~~~~
1 error generated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-11.0.6.jdk/Contents/Home
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.
Did anyone come across this error before and knows how to tackle it?

I had a problem like this with a coworker recently after they upgraded to Catalina. My solution was to install the offending version of JDK again. It looks like your system has confusion between 11.0.6 and 11.0.1.
Go to this page:
https://www.oracle.com/technetwork/java/javase/downloads/java-archive-javase11-5116896.html
Download and install 11.0.1
sudo R CMD javareconf
sudo Rstudio # elevate privs
install.packages("rJava")
If that doesn't work, try again from step 2, but with 11.0.6 from https://www.oracle.com/technetwork/java/javase/overview/index.html

What did the trick in the end was to show Rstudio where to look as identified by user Rmadillo here:
github.com/rstudio/rstudio/issues/2254
Just run this each time before using the rJava package.

"Unable to run a simple JNI program" error message when installing rJava on R 3.6 for ubuntu bionic beaver

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/).

Issues in Installing RWeka in R (Ubuntu 16.04)

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.

how to make jni.h be found?

In Ubuntu 12.04, I have jdk7 from sun/oracle installed. When locate jni.h, it prints multiple locations
/usr/lib/jvm/java-6-openjdk-amd64/include/jni.h
/usr/lib/jvm/jdk1.7.0_07/include/jni.h
...
In the header file generated by JDK, there is include <jni.h>, and currently it complains
fatal error: jni.h: No such file or directory.
In my Makefile, there is no specification of locations where jni.h is. And I am asking if possible to configure certain system parameter to make path of jni.h (say, /usr/lib/jvm/jdk1.7.0_07/include/jni.h) to be known when being compiled.

You have to tell your compiler where is the include directory. Something like this:
gcc -I/usr/lib/jvm/jdk1.7.0_07/include
But it depends on your makefile.

It needs both jni.h and jni_md.h files, Try this
gcc -I/usr/lib/jvm/jdk1.7.0_07/include \
-I/usr/lib/jvm/jdk1.7.0_07/include/linux filename.c
This will include both the broad JNI files and the ones necessary for linux

Installing the OpenJDK Development Kit (JDK) should fix your problem.
sudo apt-get install openjdk-X-jdk
This should make you able to compile without problems.

I usually define my JAVA_HOME variable like so:
export JAVA_HOME=/usr/lib/jvm/java/
Therein are the necessary include files. I sometimes add the below to my .barshrc when I compile a lot of things that need it.

Use the following code:
make -I/usr/lib/jvm/jdk*/include
where jdk* is the directory name of your jdk installation (e.g. jdk1.7.0).
And there wouldn't be a system-wide solution since the directory name would be different with different builds of JDK downloaded and installed. If you desire an automated solution, please include all commands in a single script and run the said script in Terminal.

Setting JAVA_INCLUDE_DIR to where jni.h is located should solve your problem (setting CPPFLAGS did not work for me)
Assuming it is /usr/lib64/java/include;
export JAVA_INCLUDE_DIR=/usr/lib64/java/include

For me it was a simple matter of being sure to include the JDK installation (I'd only had the JRE). My R CMD javareconf output was looking like:
Java interpreter : /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
Java version : 1.8.0_191
Java home path : /usr/lib/jvm/java-8-openjdk-amd64/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$(JAVA_HOME)/lib/amd64/server -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.o
conftest.c:1:17: fatal error: jni.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'conftest.o' failed
make: *** [conftest.o] Error 1
Unable to compile a JNI program
JAVA_HOME : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java library path:
JNI cpp flags :
JNI linker flags :
Updating Java configuration in /usr/lib/R
Done.
And indeed there was no include file in my $JAVA_HOME. Very simple remedy:
sudo apt-get install openjdk-8-jre openjdk-8-jdk
(note that this is specifically intended to install the openJDK and not the one from Oracle)
Afterwards all is well:
Java interpreter : /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java
Java version : 1.8.0_191
Java home path : /usr/lib/jvm/java-8-openjdk-amd64/jre
Java compiler : /usr/lib/jvm/java-8-openjdk-amd64/jre/../bin/javac
Java headers gen.: /usr/lib/jvm/java-8-openjdk-amd64/jre/../bin/javah
Java archive tool: /usr/lib/jvm/java-8-openjdk-amd64/jre/../bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include -I/usr/lib/jvm/java-8-openjdk-amd64/jre/../include/linux -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c conftest.c -o conftest.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR
JAVA_HOME : /usr/lib/jvm/java-8-openjdk-amd64/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/lib/R
Done.

Above answers give you a hardcoded path solution. This is bad on so many levels (java version change, OS change, etc).
Cleaner solution is to add:
JAVA_HOME = $(shell dirname $$(readlink -f $$(which java))|sed 's^jre/bin^^')
near the top of your makefile, then add:
-I$(JAVA_HOME)/include
To your include flags.
I am posting this because I ran into the same problem and spent too much time googling for wrong answers (I am building an app on multiple platforms so the build environment needs to be transportable).

None of the posted solutions worked for me.
I had to vi into my Makefile and edit the path so that the path to the include folder and the OS subsystem (in my case, -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux) was correct. This allowed me to run make and make install without issues.

In case you are on Ubuntu:
#X means 6,7,8...
apt install openjdk-X-jdk

I don't know if this applies in this case, but sometimes the file got deleted for unknown reasons, copying it again into the respective folder should resolve the problem.

error: unable to load installed packages just now

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/")'