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.oh...@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@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
