Cannot install rJava from source as "C Compiler works ... no" - r

Question

As per much of the advice on SE about getting Mac OS Sierra 10.12.4 to play with rJava nicely, the advice suggests installing from source.
However, when I try and run install.packages("rJava", type = "source") I get an output like so:
> install.packages("rJava", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-8.tar.gz'
Content type 'application/x-gzip' length 656615 bytes (641 KB)
==================================================
downloaded 641 KB
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp
checking whether the C compiler works... no
configure: error: in `/private/var/folders/lj/4s8lnxmj4_q8h65zk705k6dr0000gn/T/Rtmp4BrRQs/R.INSTALLd1278e3aab0/rJava':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/lj/4s8lnxmj4_q8h65zk705k6dr0000gn/T/RtmpFhnj89/downloaded_packages’
I've tried updating gcc and gfortran using brew, and also modified my makeconf as specified in answers here and have install xcode.
Update: I believe I have openmp installed via clang, which installed via llvm.
Upate 2: as per hrbrmstrs comment, his file at ~/.R/Makevars differed significantly from mine. Mine was I assume a default:
CC=/usr/local/opt/llvm/bin/clang -fopenmp
CXX=/usr/local/opt/llvm/bin/clang++
LDFLAGS=-L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include
And theirs was:
# shell
sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
# ~/.R/Makevars
F77 = /usr/local/gfortran/bin/gfortran
FC = /usr/local/gfortran/bin/gfortran
FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=ccache /usr/local/opt/gcc/bin/gcc-6 -Wunused-argument
CXX=ccache /usr/local/opt/gcc/bin/g++-6 -Wunused-argument
CXX1X=ccache /usr/local/opt/gcc/bin/g++-6
SHLIB_CXXLD=ccache /usr/local/opt/gcc/bin/g++-6
CCACHE_CPP=yes
CCACHE_CPP2=yes
MAKE=make -j8
Available as a gist too
Output of install.packages("rJava, type = "source") is now
> install.packages("rJava", type = "source")
trying URL 'https://cran.rstudio.com/src/contrib/rJava_0.9-8.tar.gz'
Content type 'application/x-gzip' length 656615 bytes (641 KB)
==================================================
downloaded 641 KB
* installing *source* package ‘rJava’ ...
** package ‘rJava’ successfully unpacked and MD5 sums checked
/Users/davidparr/.R/Makevars:10: *** missing separator. Stop.
/Users/davidparr/.R/Makevars:10: *** missing separator. Stop.
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 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 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...
/Users/davidparr/.R/Makevars:10: *** missing separator. Stop.
configure: error: absent
R was configured without Java support. Please run
R CMD javareconf
as root to add Java support to R.
If you do not 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 ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/lj/4s8lnxmj4_q8h65zk705k6dr0000gn/T/Rtmp7beCd4/downloaded_packages’
Now, when I try to run R CMD javareconf -e as suggested (I am not in root user), I get the following in the terminal.
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
ccache /usr/local/opt/gcc/bin/gcc-6 -Wunused-argument -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c conftest.c -o conftest.o
make: ccache: No such file or directory
make: *** [conftest.o] Error 1
Unable to compile a JNI program
I definately have a file gcc-6 in the location specified. Why is the line CXX=ccache /usr/local/opt/gcc/bin/g++-6 -Wunused-argument not CXX=/usr/local/opt/gcc/bin/g++-6?
Running sudo R CMD javareconf with and without -e is more optimistic, though I still don't understand the significance of -e:
Java interpreter : /usr/bin/java
Java version : 1.8.0_131
Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on macOS
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
/usr/local/opt/gcc/bin/gcc-6 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c conftest.c -o conftest.o
/usr/local/opt/gcc/bin/gcc-6 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

Answer 1

FWIW, I recently encountered this problem on Mac trying to upgrade from 3.4.x to 3.5.1.
My 3.4.x install had come from https://cran.r-project.org/ but I had used brew install r to upgrade.
install.packages('rJava') was refusing to work with the same error message as here:
configure: error: C compiler cannot create executables
I came here and was skeptical of changing anything in my Makevars because I already had rJava up and running on my machine for about a year on 3.4.x; in fact my .R folder was empty.
I finally concluded that the brew install was the source of my issues (or at least, that some unresolved & hidden mix-up was happening behind the scenes between my old & new installs) & installed from the CRAN website's .pkg file & this issue went away immediately.
Hopefully this experience can be helpful to some others as well.