I'm trying to use packages that require Rcpp in R on my M1 Mac, which I was never able to get up and running after purchasing this computer. I updated it to Monterey in the hope that this would fix some installation issues but it hasn't. I tried running the Rcpp check from this page but I get the following error:
> Rcpp::sourceCpp("~/github/helloworld.cpp")
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0'
ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sourceCpp_4.so] Error 1
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/RcppArmadillo/include" -I"/Users/afredston/github" -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c helloworld.cpp -o helloworld.o
clang++ -arch arm64 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o sourceCpp_4.so helloworld.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0 -L/opt/R/arm64/gfortran/lib -lgfortran -lemutls_w -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error in Rcpp::sourceCpp("~/github/helloworld.cpp") :
Error 1 occurred building shared library.
I get that it can't "find" gfortran. I installed this release of gfortran for Monterey. When I type which gfortran into Terminal, it returns /opt/homebrew/bin/gfortran. (Maybe this version of gfortran requires Xcode tools that are too new—it says something about 13.2 and when I run clang --version it says 13.0—but I don't see another release of gfortran for Monterey?)
I also appended /opt/homebrew/bin: to PATH in R so it looks like this now:
> Sys.getenv("PATH")
[1] "/opt/homebrew/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin:/Applications/RStudio.app/Contents/MacOS/postback"
Other things I checked:
Xcode command line tools is installed (which clang returns /usr/bin/clang).
Files ~/.R/Makevars and ~/.Renviron don't exist.
Here's my session info:
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.1 tools_4.1.1 RcppArmadillo_0.10.7.5.0
[4] Rcpp_1.0.7
Background
Currently (2023-02-20), CRAN builds R 4.2 binaries for Apple silicon using Apple clang from Command Line Tools for Xcode 13.1 and using an experimental fork of GNU Fortran 12.
If you obtain R from CRAN (i.e., here), then you need to replicate CRAN's compiler setup on your system before building R packages that contain C/C++/Fortran code from their sources (and before using Rcpp, etc.). This requirement ensures that your package builds are compatible with R itself.
A further complication is the fact that Apple clang doesn't support OpenMP, so you need to do even more work to compile programs that make use of multithreading. You could circumvent the issue by building R itself and all R packages from sources with LLVM clang, which does support OpenMP, but that approach is onerous and "for experts only".
There is another approach that has been tested by a few people, including Simon Urbanek, the maintainer of R for macOS. It is experimental and also "for experts only", but it works on my machine and is much simpler than learning to build R yourself.
Instructions for obtaining a working toolchain
Warning: These come with no warranty and could break at any time. Some level of familiarity with C/C++/Fortran program compilation, Makefile syntax, and Unix shells is assumed. Everyone is encouraged to consult official documentation, which is more likely to be maintained than answers on SO. As usual, sudo at your own risk.
I will try to address compilers and OpenMP support at the same time. I am going to assume that you are starting from nothing. Feel free to skip steps you've already taken, though you might find a fresh start helpful.
I've tested these instructions on a machine running Big Sur, and at least one person has tested them on a machine running Monterey. I would be glad to hear from others.
Download an R 4.2 binary from CRAN here and install. Be sure to select the binary built for Apple silicon.
Run
$ sudo xcode-select --install
in Terminal to install the latest release version of Apple's Command Line Tools for Xcode, which includes Apple clang. You can obtain earlier versions from your browser here. However, the version that you install should not be older than the one that CRAN used to build your R binary.
Download the gfortran binary recommended here and install by unpacking to root:
$ curl -LO https://mac.r-project.org/tools/gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz
$ sudo tar xvf gfortran-12.0.1-20220312-is-darwin20-arm64.tar.xz -C /
$ sudo ln -sfn $(xcrun --show-sdk-path) /opt/R/arm64/gfortran/SDK
The last command updates a symlink inside of the gfortran installation so that it points to the SDK inside of your Command Line Tools installation.
Download an OpenMP runtime suitable for your Apple clang version here and install by unpacking to root. You can query your Apple clang version with clang --version. For example, I have version 1300.0.29.3, so I did:
$ curl -LO https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
$ sudo tar xvf openmp-12.0.1-darwin20-Release.tar.gz -C /
After unpacking, you should find these files on your system:
/usr/local/lib/libomp.dylib
/usr/local/include/ompt.h
/usr/local/include/omp.h
/usr/local/include/omp-tools.h
Add the following lines to $(HOME)/.R/Makevars, creating the file if necessary.
CPPFLAGS += -I/usr/local/include -Xclang -fopenmp
LDFLAGS += -L/usr/local/lib -lomp
Run R and test that you can compile a program with OpenMP support. For example:
if (!requireNamespace("RcppArmadillo", quietly = TRUE))
install.packages("RcppArmadillo")
Rcpp::sourceCpp(code = '
#include <RcppArmadillo.h>
#ifdef _OPENMP
# include <omp.h>
#endif
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::export]]
void omp_test()
{
#ifdef _OPENMP
Rprintf("OpenMP threads available: %d\\n", omp_get_max_threads());
#else
Rprintf("OpenMP not supported\\n");
#endif
}
')
omp_test()
OpenMP threads available: 8
If the C++ code fails to compile, or if it compiles without error but you get linker warnings or you find that OpenMP is not supported, then one of us has probably made a mistake. Please report any issues.
References
Everything is a bit scattered:
R Installation and Administration manual [link]
R for macOS Developers page [link]
I resolved this issue by adding a path to the homebrew installation of gfortran to my ~/.R/Makevars following these instructions: https://pat-s.me/transitioning-from-x86-to-arm64-on-macos-experiences-of-an-r-user/#gfortran
I just avoided the issue until MacOS had things working more smoothly. so I either Windows Developer Virtual Machine (VM) or run my code development in another environment. I'm not too impressed with the updated and "faster" chipset, but that it doesn't work with much. Slow to implement and work-a-rounds often are a must.
Tested the following process for making multithread data.table work in a M2 MacBook Pro (macOS Monterey)
Steps are mostly the same with this answer by the user inferator.
Download and install R from CRAN
Download and install RStudio with developer tools
Run the following commands in terminal to install OpenMP
curl -O https://mac.r-project.org/openmp/openmp-12.0.1-darwin20-Release.tar.gz
sudo tar fvxz openmp-12.0.1-darwin20-Release.tar.gz -C /
Add compiler flags to connect clan w/ OpenMP. In terminal, write the following:
cd ~
mkdir .R
nano .R/Makevars
Inside the opened Makevars file paste the following lines. Once finished, hit command+O and then Enter to save. Do a command+X to close the editor.
CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp
Download and run the installer for gfortran by downloading gfortran-ARM-12.1-Monterey.dmg from the respective GitHub repo
This concludes the steps regarding enabling OpenMP and (hopefully) Rcpp in R under a M2 chip system.
Now, for testing that everything works with data.table I did the following
Open RStudio and run
install.packages("data.table", type = "source")
If everything is done correctly, the package should compile without any errors and return the following when running getDTthreads(verbose = TRUE):
OpenMP version (_OPENMP) 201811
omp_get_num_procs() 8
R_DATATABLE_NUM_PROCS_PERCENT unset (default 50)
R_DATATABLE_NUM_THREADS unset
R_DATATABLE_THROTTLE unset (default 1024)
omp_get_thread_limit() 2147483647
omp_get_max_threads() 8
OMP_THREAD_LIMIT unset
OMP_NUM_THREADS unset
RestoreAfterFork true
data.table is using 4 threads with throttle==1024. See ?setDTthreads.
[1] 4
I tried with the example modules given from Qt. and I downloaded the qt-everywhere-opensource-src-5.9.3 tar file and extract it.
then I run the following command.
./configure -v -prefix $PWD/qtbase -commercial -nomake tests -opengl
es2 -egl
but I got these errors.
Note: Also available for Linux: linux-clang linux-icc
Note: Dropped compiler flags '-pthread' when detecting library 'glib'.
Note: Disabling X11 Accessibility Bridge: D-Bus or AT-SPI is missing.
Note: No wayland-egl support detected. Cross-toolkit compatibility disabled.
ERROR: Feature 'egl' was enabled, but the pre-condition '(features.opengl || features.openvg) && (features.angle || libs.egl)' failed.
EGL related libraries installed on the system.
Qt: 5.9.3
Qt Creator: 4.4.1
OS: Ubuntu 16.04
GPU: Intel Haswell
libva: 1.7.0
VA-API: 0.39.0
You're probably missing some packages. If you want wayland, you're most likely going to need dev packages for libwayland and libwayland-egl, but I'm not sure what they're called on Ubuntu.
I am working on a Mac with Yosemite OS X and I'm trying to compile a program in C that I could then upload onto my Arduino. I am following a tutorial.
I tried going through and reinstalling avr-gcc, but I got the same output. I tried searching for the file crtatmega328p.o on my system, but it is nowhere to be found and the same goes for the directory.
$ avr-gcc -Os -DF_CPU=16000000UL -mmcu=atmega328p -c -o Program.o Program.c
$ avr-gcc -mmcu=atmega328p Program.o -o Program
/usr/local/lib/gcc/avr/5.2.0/../../../../avr/bin/ld: cannot find crtatmega328p.o: No such file or directory
/usr/local/lib/gcc/avr/5.2.0/../../../../avr/bin/ld: cannot find -latmega328p
collect2: error: ld returned 1 exit status
I was just hit by this issue on GNU/Linux last week.
Actually, the compiler works fine. The cause of the issue is a failed linking attempt against avr-libc.
avr-libc-1.8.1 is simply too old to work with GCC 5. Although 1.8.1 is the latest version of avr-libc, but it was released one year ago... The developing version of avr-libc has updated to catch up GCC 5, you could clone the subversion repository:
svn co svn://svn.savannah.nongnu.org/avr-libc/trunk
and compile it by yourself. If you are not familiar about how to compile yourself home-made toolchains from the source code, there are plenty of documentation and tutorial on the web.
I'm trying to cross compile Qt 5.0.1 (latest release at the moment) for my Raspberry Pi. My set up is as follows:
Operating System: Ubuntu 12.04 32-bit
Cross compiler: Built from crosstool-NG program, using the exact instructions found here
Raspberry Pi Operating System: Raspbian Wheezy 2013-02-09 (mounted at /mnt/raspberry-pi-rootfs)
Configure command:
./configure -no-pch -opengl es2 -device linux-rasp-pi-g++ -device-option CROSS_COMPILE=/home/<myusername>/x-tools/arm-unknown-linux-gnueabi/bin/arm-unknown-linux-gnueabi- -sysroot /mnt/raspberry-pi-rootfs -opensource -confirm-license -optimized-qmake -reduce-exports -release -make libs -prefix /usr/local/qt5-raspberry-pi -v
When I run the configure command, it always fails with the following error:
Could not determine the target architecture!
/mnt/raspberry-pi-rootfs/usr/include/features.h:323:26: fatal error: bits/predefs.h: No such file or directory
Anyone know what this means?
I have tried the latest pre-built Linaro Toolchain cross compiler from here, and Qt at least builds, but any program compiled with it causes SIGILL (illegal instruction) fault as soon as the program runs up, which I guess is because the pre-built cross compler I used is not targeting the right architecture.
Note:
I am aware cross compiling is fiendishly difficult, but I'd like to understand more about what is going on
I'm not sure what the exact cause of this message was, but I managed to sort out by using a pre-buils toolchain for the Raspberry Pi from here:
https://github.com/raspberrypi/tools
I'm having problems installing QT on my MacBook with Lion 10.7.3 and XCode 4.3.1 installed. I tried to install with brew, and got a compiler error. Below is the end of the error, and the "brew doctor" output. It seems to be using the wrong version of gcc... although I just installed the latest XCode. Any ideas? I'm trying to install QT, so I can run headless browser tests with capybara-webkit. (I also tried with --install-from-source and got the same error.)
gstroup$ brew install qt
....
kernel/qcocoaview_mac.mm:1386:61: error: cannot initialize a parameter of type 'NSString *' with an lvalue of type 'const NSString *'
return [[[NSAttributedString alloc] initWithString:tmpString] autorelease];
^~~~~~~~~
/System/Library/Frameworks/Foundation.framework/Headers/NSAttributedString.h:28:34: note: passing argument to parameter 'str' here
- (id)initWithString:(NSString )str;
^
2 errors generated.
make[2]: [.obj/release-shared/qcocoaview_mac.o] Error 1
make[1]: [release] Error 2
make: ** [sub-gui-make_default-ordered] Error 2
==> Exit Status: 2
http://github.com/mxcl/homebrew/blob/master/Library/Formula/qt.rb#L76
==> Environment
/usr/bin/gcc
HOMEBREW_VERSION: 0.8
HEAD: 64e489663add868db679cca2186ff8d7796e5d9e
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_LIBRARY_PATH: /usr/local/Library/Homebrew
Hardware: 8-core 64-bit dunno
OS X: 10.7.3
Kernel Architecture: x86_64
Ruby: 1.8.7-249
/usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
Xcode: 4.3.1
GCC-4.0: N/A
GCC-4.2: build 401 (5664 or newer recommended)
LLVM: build 2336
MacPorts or Fink? false
X11 installed? true
==> Build Flags
CC: /usr/bin/cc => /usr/bin/clang
CXX: /usr/bin/c++ => /usr/bin/clang
LD: /usr/bin/cc => /usr/bin/clang
CFLAGS: -O3 -w -pipe
CXXFLAGS: -O3 -w -pipe -fvisibility=hidden
MAKEFLAGS: -j8
Error: Failed executing: make
Please report this bug: https://github.com/mxcl/homebrew/wiki/new-issue
Also try:
brew doctor to check your setup for common problems.
brew missing to check installed packages for missing deps.
gstroup$ brew doctor
/usr/bin/gcc
Your gcc 4.2.x version is older than the recommended version. It may be advisable
to upgrade to the latest release of Xcode.
We couldn't detect gcc 4.0.x. Some formulae require this compiler.
/usr/bin is in your PATH before Homebrew's bin. This means that system-
provided programs will be used before Homebrew-provided ones. This is an
issue if you install, for instance, Python.
Consider editing your .bashrc to put:
/usr/local/bin
ahead of /usr/bin in your $PATH.
Some brews install binaries to sbin instead of bin, but Homebrew's
sbin was not found in your path.
Consider editing your .bashrc to add:
/usr/local/sbin
to $PATH.
/usr/bin/gcc
gstroup$ gcc --version
i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.9.00)
Copyright (C) 2007 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Xcode 4.3.x switched away from gcc as the compiler. Now Apple uses llvm. This maybe the root of your issue. There is a Github project https://github.com/kennethreitz/osx-gcc-installer/downloads that will let you download a gcc compiler.
You may have to prefix your brew command with env CC=/usr/bin/gcc to specify the gcc compiler.