[R-SIG-Mac] rJava compilation on R 3.5 devel

[Keith O'Hara]

Sorry, ignore the installation question, I missed the ‘brew install’ line. 

Try adding a symbolic link from the brew install of libomp to /usr/local/lib.



> On Jan 31, 2018, at 5:38 AM, Keith O'Hara <keith.ohara at nyu.edu> wrote:
> 
> Apple’s LLVM doesn’t support OpenMP, which explains the second error.
> 
> How did you install clang-5.0.1? If you installed using MacPorts, then you might need to create a symbolic link to libomp in /usr/local/lib. Check if the following exists:
> 
> /opt/local/lib/libomp/libomp.dylib
> 
> 
> 
>> On Jan 31, 2018, at 5:22 AM, Marc Girondot via R-SIG-Mac <r-sig-mac at r-project.org> wrote:
>> 
>> Dear Experts,
>> 
>> I use now r-3.5 devel as it is stable (from http://r.research.att.com , version (2018/01/30, r74185) ) but I have a problem with compilation of rJava package.
>> 
>> In short (all the explanations are bellow):
>> 
>> If I use clang 4.0.0 from here: http://r.research.att.com/libs/, I get this error: ld: library not found for -lomp
>> 
>> If I use clang from xcode, I get this error: clang: error: unsupported option '-fopenmp'
>> 
>> If I use clang 5.0.1, I get this error: ld: library not found for -lomp
>> 
>> Any idea to have rJava in r-devel ?
>> 
>> Thanks a lot
>> 
>> Marc
>> 
>> 
>> 
>> First I ran:
>> 
>> sudo R CMD javareconf
>> 
>> I have the Java version     : 1.8.0_162
>> 
>> I need to compile it from source but it failed with clang4 reporting an error.
>> 
>> I try various origin of clang:
>> 
>> at the beginning of the compilation, it said:
>> 
>> checking for gcc... /usr/local/clang4/bin/clang
>> 
>> I tried several version of clang:
>> 
>> belinda:local marcgirondot$ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang --version
>> Apple LLVM version 9.0.0 (clang-900.0.39.2)
>> Target: x86_64-apple-darwin17.3.0
>> Thread model: posix
>> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>> 
>> or (same version installed by: brew install llvm )
>> 
>> belinda:local marcgirondot$ /Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin/bin/clang --version
>> clang version 5.0.1 (tags/RELEASE_501/final)
>> Target: x86_64-apple-darwin17.3.0
>> Thread model: posix
>> InstalledDir: /Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin/bin
>> 
>> or
>> 
>> belinda:local marcgirondot$ /usr/local/clang4/bin/clang --version
>> clang version 4.0.0 (tags/RELEASE_400/final)
>> Target: x86_64-apple-darwin17.3.0
>> Thread model: posix
>> InstalledDir: /usr/local/clang4/bin
>> 
>> If I use the former, I get this error:
>> /usr/local/clang4/bin/clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o  -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 -lz -licucore -lm -liconv
>> ld: library not found for -lomp
>> clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
>> make[2]: *** [libjri.jnilib] Error 1
>> make[1]: *** [src/JRI.jar] Error 2
>> make: *** [jri] Error 2
>> ERROR: compilation failed for package ‘rJava’
>> 
>> Then I tried more recent versions:
>> 
>> I make a symbolic link to clang 5.0.1 or the one within xcode:
>> cd /usr/local
>> sudo ln -s /Applications/clang+llvm-5.0.1-final-x86_64-apple-darwin clang4
>> 
>> I get this error: (after running sudo R and within R: install.packages("rJava")
>> /usr/local/clang4/bin/clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o  -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 -lz -licucore -lm -liconv
>> ld: library not found for -lomp
>> clang-5.0: error: linker command failed with exit code 1 (use -v to see invocation)
>> make[2]: *** [libjri.jnilib] Error 1
>> make[1]: *** [src/JRI.jar] Error 2
>> make: *** [jri] Error 2
>> ERROR: compilation failed for package ‘rJava’
>> 
>> 
>> If I make the symbolic link to
>> cd /usr/local
>> sudo ln -s /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr clang4
>> 
>> I get this error: (after running sudo R and within R: install.packages("rJava")
>> /usr/local/clang4/bin/clang -o libjri.jnilib Rengine.o jri.o Rcallbacks.o Rinit.o globals.o rjava.o  -dynamiclib -framework JavaVM -fopenmp -L/usr/local/lib -F/Library/Frameworks/R.framework/.. -framework R -lpcre -llzma -lbz2 -lz -licucore -lm -liconv
>> clang: error: unsupported option '-fopenmp'
>> make[2]: *** [libjri.jnilib] Error 1
>> make[1]: *** [src/JRI.jar] Error 2
>> make: *** [jri] Error 2
>> ERROR: compilation failed for package ‘rJava’
>> 
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