[R-SIG-Mac] rJava compilation on R 3.5 devel [NOt completely SOLVED]
Marc Girondot
marc.girondot at u-psud.fr
Wed Jan 31 16:52:44 CET 2018
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
>>> _______________________________________________
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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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