[R-SIG-Mac] rJava compilation on R 3.5 devel [NOt completely SOLVED]

Keith O'Hara keith.ohara at nyu.edu
Wed Jan 31 14:39:44 CET 2018


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’
>>>>> 
>>>>> _______________________________________________
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>>>>> R-SIG-Mac at r-project.org
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>> 
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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
> 



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