[R-SIG-Mac] rJava compilation on R 3.5 devel [NOt completely SOLVED]
Simon Urbanek
simon.urbanek at R-project.org
Wed Jan 31 19:49:17 CET 2018
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.girondot at 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.girondot at 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.ohara at 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 at 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 at r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
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>>>
>>> --
>>> __________________________________________________________
>>> 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.girondot at 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.girondot at u-psud.fr
> Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
> Skype: girondot
>
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