Looks like something is overriding R's ldpaths settings. (R_JAVA_LD_LIBRARY_PATH should be exported with DYLD_FALLBACK_LIBRARY_PATH.)
Do you have any old .Renviron files lying around? Particularly in your home directory (~) > On Jan 31, 2018, at 2:48 PM, Marc Girondot <marc.giron...@u-psud.fr> wrote: > > Hi Simon, > > Half solution ! Thanks ! > > I remove JAVA_HOME and when R is ran as root or non-root in terminal, rJava > package can be loaded. Great ! > > But in Rstudio, I have still a problem (see bellow). > > Any suggestion ? > > Thanks > > Marc > > > 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 > > > Here are the Sys.getenv() in the 3 cases (terminal R, root or not, and > Rstudio): > Rstudio > > DYLD_FALLBACK_LIBRARY_PATH > /Library/Frameworks/R.framework/Resources/lib:/Library/Frameworks/R.framework/Resources/lib:/Users/marcgirondot/lib:/usr/local/lib:/usr/lib:::: > DYLD_LIBRARY_PATH > /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server > > R (in terminal, non-root) > > DYLD_FALLBACK_LIBRARY_PATH > /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server > > R (in terminal, root) > > DYLD_FALLBACK_LIBRARY_PATH > /Library/Frameworks/R.framework/Resources/lib:/Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server > > > > Le 31/01/2018 à 19:49, Simon Urbanek a écrit : >> 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 > > > -- > __________________________________________________________ > 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
