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@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’ > > _______________________________________________ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
