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

Simon Urbanek simon.urbanek at r-project.org
Wed Jan 31 22:44:46 CET 2018 

RStudio is not R, so you'll have ask ask their support how they pick up Java settings. As you can see they are not taking the correct settings from R so it may be a bug in RStudio.

Cheers,
Simon




> On Jan 31, 2018, at 2:48 PM, Marc Girondot <marc.girondot at 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.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
>>>>>> R-SIG-Mac at 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.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
>>> 
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at 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.girondot at u-psud.fr
> Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
> Skype: girondot
>

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