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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.
Community
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DaveRGP
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  • Why is this tagged gfortran? – Vladimir F Героям слава Apr 26 '17 at 12:15
  • have you seen this answer? http://stackoverflow.com/a/35852152/4389763 – CJ Yetman Apr 26 '17 at 12:21
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    `checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp` -- do you have OpenMP installed on your system? If not, that's probably why this is failing. – nrussell Apr 26 '17 at 12:36
  • @VladimirF, because other material has suggested to me that gfortran is needed to compile any R material on mac. Prior gcc you had to install it seperately to fix this issue according to some solutions. Now it's bundled in gcc by default but I assume it's still part of the process. – DaveRGP Apr 26 '17 at 12:42
  • @nrussell, I _think_ so, I tried to do it for data.table, however I'm pretty sure I didn't do it correctly. How would I check? (Sorry, really new to mac, probably really simple) – DaveRGP Apr 26 '17 at 12:43
  • Thanks @CJYetman, I have and in fact it's the first link in my question and the main reason I'm trying to build from source. – DaveRGP Apr 26 '17 at 12:45
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    @DaveRGP I don't have access to a macOS machine, so I can't really advise you on this. [This question](http://stackoverflow.com/questions/35134681/installing-openmp-on-mac-os-x-10-11) seems relevant; else I'm sure you can find it with a little googling. – nrussell Apr 26 '17 at 12:48
  • @nrussell, I've looked through that question, which is pretty old, my rabbit hole lead me to find that theoretically, openmp is included now included in clang, and clang is now itself included in llvm (all of these ideas are new to me), and I have a file at `/usr/local/opt/llvm/bin/clang`, further my R makevars look like they are set to look there under the CC argument with the flag `-fopenmp` – DaveRGP Apr 26 '17 at 13:27
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    sorry, I didn't realize "much of the advice" was three different links and I only clicked on one of them – CJ Yetman Apr 26 '17 at 14:17
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    Here's the `~/.R/Makevars` I use as well as the required symlink to get rJava to work. https://gist.github.com/hrbrmstr/6f228eead691e72bd0272a25319ea9ee (I usually do the `R CMD javareconf` first before installing `rJava`). There's a long-winded (and I've got no time) as to why the g[++] toolchain is needed vs clang and I think I've seen folks get it to work with clang but I'm g[++] is working fine for me. – hrbrmstr Apr 26 '17 at 14:24
  • @hrbrmstr, thanks a lot. This seems to have fixed the build situation. the build failed, however that was for a clearer reason. If you stick an answer in when you have time (and also explain what this changes), then I'll be happy to mark it correct and close this. – DaveRGP Apr 26 '17 at 14:36
  • @hrbrmstr, just looked at the gist again, is the one line under `#shell` for the terminal, not for the `~/.R/.Makevars` file itself? – DaveRGP Apr 26 '17 at 15:07
  • @hrbrmstr, dw, worked it out, it isn't – DaveRGP Apr 26 '17 at 15:20

1 Answers1

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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.

MichaelChirico
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