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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