It means that you are likely setting JAVA_HOME incorrectly in your user account. Don't set JAVA_HOME - you'll only likely break things by doing so.
Cheers, Simon > On Jan 31, 2018, at 10:52 AM, Marc Girondot <marc.giron...@u-psud.fr> wrote: > > Thanks for your help: > > Here are some results; First in terminal: > > belinda:~ marcgirondot$ locate libjvm.dylib > /Applications/Xcode.app/Contents/Applications/Application > Loader.app/Contents/itms/java/lib/server/libjvm.dylib > /Library/Internet > Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/lib/server/libjvm.dylib > /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries/libjvm.dylib > /Library/Java/JavaVirtualMachines/jdk1.8.0_121.jdk/Contents/Home/jre/lib/server/libjvm.dylib > /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/server/libjvm.dylib > /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server/libjvm.dylib > > Now in R as non-root: > > > Sys.getenv() > DYLD_FALLBACK_LIBRARY_PATH > /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/lib/server > > The path of DYLD_FALLBACK_LIBRARY_PATH is wrong. This folder does not exist. > > And in R as root > > Sys.getenv() > DYLD_FALLBACK_LIBRARY_PATH > /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server > > The path is correct > > Strange... but no solution still > > Marc > > > Le 31/01/2018 à 14:39, Keith O'Hara a écrit : >> 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 >>> > > -- > __________________________________________________________ > 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 _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
