Trying to get Rcpp to work on R 4.1.2 on Mac OS Monterey using an Intel computer.
> library(Rcpp)
> evalCpp("2 + 2")
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include" -I"/private/var/folders/jz/977gqfr957g_rlgw1h05152w0000gq/T/Rtmp8hmDZ5/sourceCpp-x86_64-apple-darwin17.0-1.0.8" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c file152f71a55f97c.cpp -o file152f71a55f97c.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -Wl,-rpath,/Library/Frameworks/R.framework/Resources/lib /Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o sourceCpp_2.so file152f71a55f97c.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in sourceCpp(code = code, env = env, rebuild = rebuild, cacheDir = cacheDir, :
Error 1 occurred building shared library.
clang: error: no such file or directory: '/Library/Frameworks/R.framework/Resources/lib/libc++abi.1.dylib'
make: *** [sourceCpp_2.so] Error 1
I have followed Coatless Professor's instructions:
https://thecoatlessprofessor.com/programming/cpp/r-compiler-tools-for-rcpp-on-macos/
I believe Xcode Command Line Tools and gfortran are installed:
$which gcc
/usr/bin/gcc
$which gfortran
/usr/local/bin/gfortran
and I have removed both ~/.R/Makevars and ~/.Renviron.
Any help would be much appreciated -- thanks so much!
There is an old reference to a prior version of the clang compiler present.
In R, please type:
unlink("~/.R/Makevars")
unlink("~/.Renviron")
Please restart R and, then, try:
Rcpp::evalCpp("1+1")
Related
My mac system is macOS Catalina 10.15.1, and my R version is 3.6.1. When I try to install the rJava package on Rstudio using install.packages("rJava", type="source), it comes with error:
make: *** [jri_glue.o] Error 1
ERROR: compilation failed for package ‘rJava’
* removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rJava’
Warning in install.packages :
installation of package ‘rJava’ had non-zero exit status
I have tried sudo R CMD javareconf and then reinstall the rJava package but it does not work. When I use sudo R CMD javareconf on terminal, it shows that
ava interpreter : /usr/bin/java
Java version : 13.0.2
Java home path : /Library/Java/JavaVirtualMachines/jdk-13.0.2.jdk/Contents/Home
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
trying to compile and link a JNI program
detected JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
gcc-7 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk-13.0.2.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk-13.0.2.jdk/Contents/Home/include/darwin -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -mtune=native -g -O2 -Wall -pedantic -Wconversion -c conftest.c -o conftest.o
gcc-7 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk-13.0.2.jdk/Contents/Home/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk-13.0.2.jdk/Contents/Home
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.
This problem happened before and I use this solution trouble installing and loading rJava on mac El Capitan. But when my mac is updated to Catalina 10.15.1, the solution does not work. I am not familiar with java. How to install rJava successfully in such situation?
Based on several postings in stackoverflow, in OSX 10.15, I can suppress warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness] from conftest.c by clang -Wno-nullability-completeness -o conftest -g -O2 -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include conftest.c or gcc -Wno-nullability-completeness conftest.c. But how can I implement this for compiling a whole R pacakge from the source ? I added -Wno-nullability-completeness in R Makevers like this :
CC=clang -Wno-nullability-completeness
CXX=clang++ -Wno-nullability-completeness
CFLAGS=-Wno-nullability-completeness -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-Wno-nullability-completeness -g -O3 -Wall -pedantic -std=c++11 -mtune=native
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include
but it did not work. Any suggestions or pointers will be seriously appreciated.
My system;
sw_vers
ProductName: Mac OS X
ProductVersion: 10.15.2
BuildVersion: 19C57
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/9.2.0_2/libexec/gcc/x86_64-apple-darwin19/9.2.0/lto-wrapper
Target: x86_64-apple-darwin19
Configured with: ../configure --build=x86_64-apple-darwin19 --prefix=/usr/local/Cellar/gcc/9.2.0_2 --libdir=/usr/local/Cellar/gcc/9.2.0_2/lib/gcc/9 --disable-nls --enable-checking=release --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-9 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --with-pkgversion='Homebrew GCC 9.2.0_2' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-multilib --with-native-system-header-dir=/usr/include --with-sysroot=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
Thread model: posix
gcc version 9.2.0 (Homebrew GCC 9.2.0_2)
clang -v
clang version 9.0.0 (tags/RELEASE_900/final)
Target: x86_64-apple-darwin19.2.0
Thread model: posix
InstalledDir: /usr/local/opt/llvm/bin
brew info R
R: stable 3.6.2 (bottled)
Software environment for statistical computing
https://www.r-project.org/
/usr/local/Cellar/R/3.6.2 (2,123 files, 58.5MB)
Poured from bottle on 2019-12-14 at 09:37:12
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/r.rb
==> Dependencies
Build: pkg-config ✔
Required: gcc ✔, gettext ✔, jpeg ✔, libpng ✔, openblas ✔, pcre ✔, readline ✔, xz ✔
Flags:
CPATH=/usr/local/include
LDFLAGS=-L/usr/local/opt/llvm/lib
CPPFLAGS=-I/usr/local/opt/llvm/include
SDKROOT=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk
Edit 1
From a suggestion by Ralf Stubner, I looked at an installer output generated by install.package("e1071", keep_outputs=T) ;
All my packages loaded Tue Dec 31 16:23:24 2019* installing *source* package ‘e1071’ ...
** package ‘e1071’ successfully unpacked and MD5 sums checked
** using staged installation
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++ -std=gnu++11 accepts -g... yes
** libs
clang -I"/usr/local/Cellar/r/3.6.2/lib/R/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/include **-fPIC -g -O2** -c Rsvm.c -o Rsvm.o
In file included from Rsvm.c:2:
/usr/local/include/stdio.h:67:13: warning: pointer is missing a nullability type specifier (_Nonnull, _Nullable, or _Null_unspecified) [-Wnullability-completeness]
extern FILE *__stdinp ........;
and I realized that CXXFLAGs in my Makevars may not be read by clang at all. A following is my current Makevars;
LLVM_LOC = /usr/local/opt/llvm
CC=clang
CXX=clang++
CXX11=clang++
CFLAGS = -g -O3 -Wall -pipe -pedantic -Wno-nonnull -std=gnu99 -mtune=native
CXXFLAGS = -g -O3 -Wall -pipe -Wno-nonnull -pedantic -std=c++11 -mtune=native
CXX11FLAGS = -g -O3 -Wall -pipe -Wno-nonnull -pedantic -std=c++11 -mtune=native
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include
Ok I figured this out. Thanks to the help from RalfStubner. I realized that I was not putting Makevars in the right location. A default location of Makevars should be ~/.R/Makevars. Now, CXXFLAGS in the Makevars is read and -Wno-nonnull is applied. My latest Makevars is as follows;
LLVM_LOC = /usr/local/opt/llvm
CC=$(LLVM_LOC)/bin/clang -fopenmp
CXX=$(LLVM_LOC)/bin/clang++ -fopenmp
CC=clang
CXX=clang++
CXX11=clang++
CFLAGS = -g -O3 -Wall -pipe -pedantic -Wno-nonnull -std=gnu99 -mtune=native -pipe
CXXFLAGS = -g -O3 -Wall -pipe -Wno-nonnull -pedantic -std=c++11 -mtune=native
CXX11FLAGS = -g -O3 -Wall -pipe -Wno-nonnull -pedantic -std=c++11 -mtune=native
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include
I am trying to compile a program mafTools on MacOSX using gnu make. I get the following error:
cd mafExtractor && make all
clang -std=c99 -stdlib=libstdc++ -O3 -c -O3 -Wall -Werror --pedantic -funroll-loops -DNDEBUG -Wshadow -Wpointer-arith -Wstrict-prototypes -Wmissing-prototypes -I ../../sonLib/lib -I ../inc -I ../external src/mafExtractorAPI.c -o src/mafExtractorAPI.o.tmp -lm
This gives the error:
clang: error: -lm: 'linker' input unused [-Werror,-Wunused-command-line-argument]
make[1]: \*** [src/mafExtractorAPI.o] Error 1
make: \*** [mafExtractor.all] Error 2
I looked at similar errors but couldn't fix it. Any help will be much appreciated. Thanks!
This is the package: https://github.com/dentearl/mafTools/tree/master/mafExtractor
Everything else here compiled successfully.
This is the makefile:
https://github.com/dentearl/mafTools/blob/master/mafExtractor/Makefile
Thanks a bunch.
Your clang commaand includes the -c option which means you do not want to link and resolve external references, you just want to produce an unlinked object file.
Your -lm option says you want to link with the maths library.
Basically, the aforementioned options are incompatible - you cannot both link with the math library and not link.
TLDR; Remove -lm
I have recently installed R 3.1.3. I am using a Mac with Yosemite system and my Xcode is of version 6.2.
After I source the CPP file using sourceCpp("try.cpp"), I get the following error. My try.cpp file has
#include <RcppArmadillo.h>
#include <math.h>
The error is below in R
ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lquadmath
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_15736.so] Error 1
clang++ -arch x86_64 -ftemplate-depth-256 -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RcppArmadillo/include" -fPIC -mtune=core2 -O3 -c CAR.cpp -o CAR.o
clang++ -arch x86_64 -ftemplate-depth-256 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module - multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib - L/usr/local/lib -o sourceCpp_15736.so CAR.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in sourceCpp("~/RA2015/Code/BYMCAR/CAR.cpp") :
Error 1 occurred building shared library.
WARNING: The tools required to build C++ code for R were not found.
Please install Command Line Tools for XCode (or equivalent).
I have installed the command line tools for Xcode, my gfortran version is 4.9.0
But when I type
gfortran --version
It has the following error:
gfortran: warning: couldn’t understand kern.osversion ‘14.1.0
When I use R 3.1.2, I did not encounter this problem before!
Any help is appreciated!
After some finding I find a solution online.
If you have same problem with me, just type
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
on the terminal and sourceCpp can run smoothly.
A detailed explanation can be found at [http://www.thecoatlessprofessor.com/programming/rcpp-rcpparmadillo-and-os-x-mavericks-lgfortran-and-lquadmath-error]
i'm trying to install the scikit-learn-0.14.1 in my osx 10.6.8 but as i've been told, i have to install numpy and scipy before. However i'm getting the following error msg when i try to run each one installation setup.py program. what should i do?
NumPY-1.8.1
File "numpy/core/setup.py", line 682, in get_mathlib_info
raise RuntimeError("Broken toolchain: cannot link a simple C program")
RuntimeError: Broken toolchain: cannot link a simple C program
SciPY-0.14.0
ValueError: numpy >= 1.4 is required (detected 1.2.1 from /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy/init.pyc)
Scikit-learn-0.14.1
error: Command "g++-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -Os -Wall -DENABLE_DTRACE -arch i386 -arch ppc -arch x86_64 -pipe -c sklearn/svm/src/libsvm/libsvm_template.cpp -o build/temp.macosx-10.6-universal-2.6/sklearn/svm/src/libsvm/libsvm_template.o" failed with exit status 127
Easier to downloand the Anaconda distribution. https://store.continuum.io/cshop/anaconda/