[R-SIG-Mac] rJava compilation on R 3.5 devel [NOt completely SOLVED]
Keith O'Hara
keith.ohara at nyu.edu
Wed Jan 31 22:39:06 CET 2018
Looks like something is overriding R's ldpaths settings. (R_JAVA_LD_LIBRARY_PATH should be exported with DYLD_FALLBACK_LIBRARY_PATH.)
Do you have any old .Renviron files lying around? Particularly in your home directory (~)
> 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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