Problems installing R package "nloptr" on M1 mac

Question

I'm trying to install the "lme4" library in R and RStudio, which worked before I was on an M1 Mac, but now it's not installing. The dependency that's having trouble is: "nloptr". Here's my current error:

clang++ -arch arm64 -std=gnu++11 -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 nloptr.so init_nloptr.o nloptr.o test-C-API.o test-runner.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 -Lnlopt/lib -lnlopt -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-Lnlopt/lib'
ld: library not found for -lnlopt
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/nloptr’
Warning in install.packages :
  installation of package ‘nloptr’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/ht/y6qd6yfn67x086jtwxvh42tw0000gn/T/RtmpULtpZq/downloaded_packages’ ```

I'm on an M1 Mac with Monterey (12.1). I've installed the arm64 version of R. Here's my current version R 4.1.2:

> version
               _                           
platform       aarch64-apple-darwin20      
arch           aarch64                     
os             darwin20                    
system         aarch64, darwin20           
status                                     
major          4                           
minor          1.2                         
year           2021                        
month          11                          
day            01                          
svn rev        81115                       
language       R                           
version.string R version 4.1.2 (2021-11-01)
nickname       Bird Hippie

I've already tried the following in Terminal: brew install nlopt and brew install gcc.

Before this, I also had an error as follows: ld: warning: directory not found for option '-L/opt/R/arm64/gfortran/lib/gcc/aarch64-apple-darwin20.2.0/11.0.0' To fix that, based on Googling, I did this export PATH=$PATH:/opt/R/arm64/gfortran/bin and this ln -sfn `xcrun --show-sdk-path` /opt/R/arm64/gfortran/SDK

If it continues to not work, it might be worth posting an issue at https://github.com/astamm/nloptr/issues — Ben Bolker, Jan 27 '22 at 16:57

Mikael Jagan · Accepted Answer · 2022-01-28T17:49:48.683

On my machine (an M1 Mac running Big Sur), I've just tried install.packages("nloptr") without first doing brew install nlopt.

I get the same warning about -Lnlopt/lib:

ld: warning: directory not found for option '-Lnlopt/lib'
ld: library not found for -lnlopt
clang-13: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [nloptr.so] Error 1
ERROR: compilation failed for package ‘nloptr’

but prior to the warning I see:

checking if pkg-config knows NLopt... no
using NLopt via local cmake build on arm64

------------------ CMAKE NOT FOUND --------------------

CMake was not found on the PATH. Please install CMake:

 - yum install cmake          (Fedora/CentOS; inside a terminal)
 - apt install cmake          (Debian/Ubuntu; inside a terminal).
 - pacman -S cmake            (Arch Linux; inside a terminal).
 - brew install cmake         (MacOS; inside a terminal with Homebrew)
 - port install cmake         (MacOS; inside a terminal with MacPorts)

Alternatively install CMake from: <https://cmake.org/>

-------------------------------------------------------

install.packages("nloptr") succeeds after I install CMake with brew install cmake.

As for your initial issue with gfortran, I might suggest trying my instructions here. R recommends installing a specific build of gfortran and configuring compilers to find that installation via ~/.R/Makevars. You really should not need to mess with your PATH...

score 1 · Answer 2 · answered Aug 10 '22 at 17:21

Unfortunately brew install cmake didn't help me, nor did installing nloptr from source, nor did configuring RStudio to use the correct PATH.

According to the documentation, in the section labeled Installing CMake (macOS and Linux only), the nloptr package installer expects to find the cmake executable either at:

The path specified by the CMAKE_BIN environment variable (spoiler alert: setting it didn't work), or
/Applications/CMake.app/Contents/bin/cmake.

Here's how I finally resolved the problem in a zsh shell:

brew install cmake
sudo mkdir -p /Applications/cmake.app/Contents/bin
cd /Applications/cmake.app/Contents/bin
sudo ln -s /opt/homebrew/bin/cmake

The downside to this approach is that it puts a non-application in the /Applications directory, but that I can live with.

Problems installing R package "nloptr" on M1 mac

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