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R-Project: xlsx package installation failure (due to java issues)

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/

GCC option not found while constructing .dll

I'm trying to create a .dll while following this tutorial (http://www3.ntu.edu.sg/home/ehchua/programming/java/JavaNativeInterface.html) to use JNI in my eclipse project. There's an issue with my makefile however that may be unrelated to all the JNI stuff.
I'm getting "unknown option: --add-stdcall-alias" when I build (make all). I'm using the Mac GCC Compiler. Here's my console log and make file:
EDIT: So i removed the option that is giving me the error and my build worked. However, I feel unsafe just removing a line of code that I am clueless about. Any one want to tell me the implications of removing this code?
console output:
18:05:33 ** Build of configuration Default for project HPA* Testing *
make all
javah -classpath ../bin HPAProgram
gcc -Wl,--add-stdcall-alias -shared -o hpaprogram.dll HPAProgram.o
ld: unknown option: --add-stdcall-alias
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: ** [hpaprogram.dll] Error 1
18:05:34 Build Finished (took 823ms)
makefile:
# Define a variable for classpath
CLASS_PATH = ../bin
# Define a virtual path for .class in the bin directory
vpath %.class $(CLASS_PATH)
all : hpaprogram.dll
# $# matches the target, $< matches the first dependancy
hpaprogram.dll : HPAProgram.o
gcc -Wl,--add-stdcall-alias -shared -o $# $<
# $# matches the target, $< matches the first dependancy
HPAProgram.o : HPAProgram.c++ HPAProgram.h
gcc -I /System/Library/Frameworks/JavaVM.framework/Versions/A/Headers/ -c $< -o $#
# $* matches the target filename without the extension
HPAProgram.h : HPAProgram.class
javah -classpath $(CLASS_PATH) $*
clean :
rm HPAProgram.h HPAProgram.o hpaprogram.dll

I practiced by following the same tutorial, it turned out that it's OK to get rid of "-Wl,--add-stdcall-alias".
BTW, in Mac, you have to use ".dylib" instead of ".so", otherwise you will get error saying "java.lang.UnsatisfiedLinkError: no hello in java.library.path".

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.

Installing Jmagick-6.6.9 on Mac no .dylib generated

I am working to install an existing Java application on OSX 10.8 (Mountain Lion) that depends on Jmagick (and ImageMagick). When I build Jmagick 6.6.9, it successfully generates .so, but does not generate .dylib files. Any idea of why this is happening? Here is the output from config and make install.
> ./configure --prefix=/Users/mr/m4/support/jmagick/darwin/current --with-magick-home=/usr/local/Cellar/imagemagick
checking build system type... i686-apple-darwin12.2.0
checking host system type... i686-apple-darwin12.2.0
checking target system type... i686-apple-darwin12.2.0
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for a BSD-compatible install... /usr/bin/install -c
checking for getconf... /usr/bin/getconf
checking whether large file support needs explicit enabling... no
checking for X... libraries /usr/X11/lib, headers /usr/X11/include
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/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 jni.h usability... yes
checking jni.h presence... yes
checking for jni.h... yes
checking for java... /Users/mr/m4/support/java/darwin/current/bin/java
checking for javac... /Users/mr/m4/support/java/darwin/current/bin/javac
checking for javah... /Users/mr/m4/support/java/darwin/current/bin/javah
checking for jar... /Users/mr/m4/support/java/darwin/current/bin/jar
checking for javadoc... /Users/mr/m4/support/java/darwin/current/bin/javadoc
checking for MagickCore-config... /usr/local/bin/MagickCore-config
checking magick/api.h usability... yes
checking magick/api.h presence... yes
checking for magick/api.h... yes
checking for ConstituteImage in -lMagick... no
checking for a sed that does not truncate output... /usr/bin/sed
checking for ld used by gcc... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) is GNU ld... no
checking for /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... no
checking for xlf... no
checking for f77... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for xlf90... no
checking for f90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... no
checking for g95... no
checking for xlf95... no
checking for f95... no
checking for fort... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgfortran... no
checking for pgf95... no
checking for lf95... no
checking for ftn... no
checking for nagfor... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether accepts -g... no
checking the maximum length of command line arguments... 196608
checking command to parse /usr/bin/nm output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc static flag works... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fno-common
checking if gcc PIC flag -fno-common works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin12.2.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
configure: creating libtool
appending configuration tag "CXX" to libtool
rm: conftest.dSYM: is a directory
checking for ld used by g++... /usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld
checking if the linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) is GNU ld... no
checking whether the g++ linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fno-common
checking if g++ PIC flag -fno-common works... rm: conftest.dSYM: is a directory
yes
checking if g++ supports -c -o file.o... rm: conftest.dSYM: is a directory
yes
checking whether the g++ linker (/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin12.2.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
configure: creating ./config.status
config.status: creating Make.def
And make install
> make install
/usr/bin/install -c -d /Users/mr/m4/support/jmagick/darwin/current/lib
/usr/bin/install -c /Users/mr/m4/support/jmagick/trunk/lib/jmagick-6.6.9.jar /Users/mr/m4/support/jmagick/darwin/current/lib
Installing /Users/mr/m4/support/jmagick/trunk ...
make[1]: Entering directory `/Users/mr/m4/support/jmagick/trunk/src'
Installing /Users/mr/m4/support/jmagick/trunk/src ...
make[2]: Entering directory `/Users/mr/m4/support/jmagick/trunk/src/magick'
/usr/bin/install -c -d /Users/mr/m4/support/jmagick/darwin/current/lib
/bin/sh /Users/mr/m4/support/jmagick/trunk/libtool --mode=install /usr/bin/install -c /Users/mr/m4/support/jmagick/trunk/lib/libJMagick-6.6.9.so /Users/mr/m4/support/jmagick/darwin/current/lib
/usr/bin/install -c /Users/mr/m4/support/jmagick/trunk/lib/libJMagick-6.6.9.so /Users/mr/m4/support/jmagick/darwin/current/lib/libJMagick-6.6.9.so
Installing /Users/mr/m4/support/jmagick/trunk/src/magick ...
make[3]: Entering directory `/Users/mr/m4/support/jmagick/trunk/src/magick/util'
Installing /Users/mr/m4/support/jmagick/trunk/src/magick/util ...
make[3]: Leaving directory `/Users/mr/m4/support/jmagick/trunk/src/magick/util'
Using install_name_tool...
make[2]: Leaving directory `/Users/mr/m4/support/jmagick/trunk/src/magick'
make[1]: Leaving directory `/Users/mr/m4/support/jmagick/trunk/src'
Output files:
> pwd
/Users/mr/m4/support/jmagick/darwin/current
> ls -AR
lib
./lib:
jmagick-6.6.9.jar libJMagick-6.6.9.so libJMagick.so
Imagemagic6.6.9-10 was installed using Homebrew:
> brew info imagemagick
imagemagick: stable 6.6.9-10, HEAD
http://www.imagemagick.org
Depends on: jpeg, libtiff, little-cms, jasper
/usr/local/Cellar/imagemagick/6.6.9-10 (1394 files, 32M) *
https://github.com/mxcl/homebrew/commits/master/Library/Formula/imagemagick.rb

You should also make something like this:
sudo ln -s /Path/to/libJMagick.so /Path/to/Java/Extensions/libJMagick.dylib
Same for libJMagick-6.6.9.so
Add it to your project and try to run.

Can't install rJava on ubuntu system

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.