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.giron...@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.oh...@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@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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--
__________________________________________________________
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.giron...@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.giron...@u-psud.fr
Web: http://www.ese.u-psud.fr/epc/conservation/Marc.html
Skype: girondot
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