Seems odd that R can’t find libjvm outside of sudo. From R, run
Sys.getenv() and check your DYLD_LIBRARY_PATH and DYLD_FALLBACK_LIBRARY_PATH variables. Should be ‘[..]/Home/jre/lib/server’ in there somewhere. Check those paths for libjvm.dylib > On Jan 31, 2018, at 8:17 AM, Marc Girondot <marc.giron...@u-psud.fr> wrote: > > Sorry... bad news. It works only if R is ran as root. If R is ran as non-root > user: > > > library(rJava) > Erreur : package or namespace load failed for ‘rJava’: > .onLoad a échoué dans loadNamespace() pour 'rJava', détails : > appel : dyn.load(file, DLLpath = DLLpath, ...) > erreur : impossible de charger l'objet partagé > '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so': > dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, > 6): Library not loaded: @rpath/libjvm.dylib > Referenced from: > /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so > Reason: image not found > > I will continue to investigate. > > Sorry for this wrong news ! > > Marc > > > Le 31/01/2018 à 14:03, Marc Girondot via R-SIG-Mac a écrit : >> I have found a solution based on the proposition of Keith. Thanks a lot >> >> ############ >> >> First I have made some cleaning because I had pieces of clang in many places. >> >> Then with a clean version I installed clang-4.0.0-darwin15.6-Release.tar.gz >> using the version in >> http://r.research.att.com/libs/clang-4.0.0-darwin15.6-Release.tar.gz >> >> Note that it produced an error at the end when I run the command: >> sudo tar xvzf clang-4.0.0-darwin15.6-Release.tar.gz -C / >> The error is: >> tar: Error exit delayed from previous errors. >> >> But it seems to be ok >> >> then I create the link as propose by Keith: >> cd /usr/local/lib >> sudo ln -s /usr/local/clang4/lib/libomp.dylib libomp.dylib >> >> And it works perfectly if the install.packages("rJava") is ran as root: sudo >> R >> >> ###################### >> >> Now, let try with clang 5.0.1 from homebrew. >> >> First I delete all tracks of previous installation of clang4: >> sudo cd <folder where is clang-4.0.0-darwin15.6-Release.tar.gz)> >> # I use this trick to enter the root password firsttime; after it does not >> ask within the loop >> for file in $(tar tfz clang-4.0.0-darwin15.6-Release.tar.gz); do >> sudo rm -f /$file; >> done >> >> # Remove empty _folders_ associated with the binary >> for file in $(tar tfz clang-4.0.0-darwin15.6-Release.tar.gz); do >> sudo rmdir -p /$file; >> done >> >> Then I install llvm with homebrew: >> brew install llvm >> >> in /usr/local/opt/llvm/lib there is no libomp.dylib but libgomp.dylib and >> libiomp5.dylib. I don't know if I can use it instead of libomp.dylib. >> >> But I see one in: >> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libomp.dylib >> >> Better to use this one: >> cd /usr/local/lib >> sudo ln -s >> /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libomp.dylib >> libomp.dylib >> >> >> And the compilation ran correctly. >> >> Thanks a lot ! >> >> Marc >> >> Le 31/01/2018 à 11:52, Keith O'Hara a écrit : >>> 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 > > > -- > __________________________________________________________ > Marc Girondot, Pr > > Laboratoire Ecologie, Systématique et Evolution > Equipe de Conservation des Populations et des Communautés > CNRS, AgroParisTech et Université Paris-Sud 11 , UMR 8079 > Bâtiment 362 > 91405 Orsay Cedex, France > > Tel: 33 1 (0)1.69.15.72.30 Fax: 33 1 (0)1.69.15.73.53 > e-mail: marc.giron...@u-psud.fr > Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html > Skype: girondot > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
