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

Marc Girondot marc.girondot at u-psud.fr
Wed Jan 31 14:17:09 CET 2018 

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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>
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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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