Clang-7: Error: Linker Command Failed With Exit Code 1 For Macos Big Sur

clang-7: error: linker command failed with exit code 1 for macOS Big Sur

This has been challenging, but here are the steps I used compile R packages from source on MacOS Big Sur:

1. Reinstall xcode command line tools

(don't believe Software Update if it says 'up to date' - he lies - brew doctor said my version was actually old)

sudo rm -rf /Library/Developer/CommandLineTools
sudo xcode-select --install

2. Install gcc & llvm via Homebrew (instructions for installing Homebrew) or, if you already have gcc/llvm installed, skip to the next step

# WARNING: This can take several hours
brew install gcc
brew install llvm

3. If you already have gcc & llvm installed via Homebrew:

brew cleanup
brew update
brew upgrade
brew reinstall gcc
brew reinstall llvm

4. Link some headers into /usr/local/include

sudo ln -s /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/* /usr/local/include/

# I believe you can safely ignore warnings like this:
#ln: /usr/local/include//tcl.h: File exists
#ln: /usr/local/include//tclDecls.h: File exists
#ln: /usr/local/include//tclPlatDecls.h: File exists
#ln: /usr/local/include//tclTomMath.h: File exists
#ln: /usr/local/include//tclTomMathDecls.h: File exists
#ln: /usr/local/include//tk.h: File exists
#ln: /usr/local/include//tkDecls.h: File exists
#ln: /usr/local/include//tkPlatDecls.h: File exists

5. Edit your ~/.R/Makevars file (if you don't have a file called Makevars in your ~/.R/ directory, create it) and include only these lines:

FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

LLVM_LOC = /usr/local/opt/llvm
CC=/usr/local/gfortran/bin/gcc -fopenmp
CXX=/usr/local/gfortran/bin/g++ -fopenmp
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
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/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include

6. Compile a package from source in R/Rstudio

# Compile the nlme package from source
install.packages("nlme", type = "source")

# To check whether openmp is enabled, compile data.table:
install.packages("data.table", type = "source")

Update (2022/04/05)

I had an error when updating "RcppAlgos" (couldn't find gmp.h or libgmp). I checked gmp was installed (brew install gmp), then added /usr/local/include to CPPFLAGS and /usr/local/lib to LDFLAGS in the ~/.R/Makevars file to solve the problem, i.e.

cat ~/.R/Makevars
LOC=/usr/local/gfortran
CC=$(LOC)/bin/gcc -fopenmp
CXX=$(LOC)/bin/g++ -fopenmp
CXX11 = $(LOC)/bin/g++ -fopenmp

CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L$(LOC)/lib -Wl,-rpath,$(LOC)/lib,-L/usr/local/lib
CPPFLAGS=-I$(LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/usr/local/include

FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++

clang: error: linker command failed with exit code 1 when running fishchips on macOS

I believe I found the solution fix. It seems as if deleting OMPFLAG was all that was needed to run.

error: linking with `cc` failed: exit code: 1

From your command rustc test1.rs the compiler infers the name of the executable should be test1. The linker tries to open this file so it can write the executable but fails with errno=21 whose stringified version is "Is a directory".

This suggests you have a directory in your working directory called test1 which is causing a conflict.

Big Sur clang invalid version error due to MACOSX_DEPLOYMENT_TARGET

Figure out the issue on my end.

Previously I had installed XCode from the App Store (11.7) and set its SDKs as my default:

sudo xcode-select --switch /Applications/Xcode.app/

However, it seems this come with an unsupported version of clang:

  λ clang --version
Apple clang version 11.0.3 (clang-1103.0.32.62)
Target: x86_64-apple-darwin20.1.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

Setting the xcode-select to the latest version via:

sudo xcode-select --switch /Library/Developer/CommandLineTools

EDIT (11/15/2020)

You might receive an error when attempting the above change:

xcode-select: error: invalid developer directory '/Library/Developer/CommandLineTools'

To fix this, you must install the latest Command Line Tools from the official Apple website here. At the time of writting this edit, I installed the Command Line Tools for Xcode 12.3 beta.

Changes clang to a working version:

  λ clang --version
Apple clang version 12.0.0 (clang-1200.0.32.2)
Target: x86_64-apple-darwin20.1.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

The built-in Big Sur SDK is version 10.15, which seems to work without an issue:

  λ ls /Library/Developer/CommandLineTools/SDKs
MacOSX.sdk      MacOSX10.15.sdk

After the switch, multidict was installed successfully.

  λ pip install multidict
Collecting multidict
  Downloading multidict-4.7.6-cp38-cp38-macosx_10_14_x86_64.whl (48 kB)
     |████████████████████████████████| 48 kB 589 kB/s
Installing collected packages: multidict
Successfully installed multidict-4.7.6

Further investigation seems to indicate this is a design choice by Apple (source):

Therefore, ensuring your SDK is the default out-of-the-box as opposed to XCode's new SDK should be enough for the system to switch context when needed (and seems to work fine with pip+clang).

Issues installing RcppMP in MacOS

This was a bit more complicated than I thought; this package requires mpfr, gmp and the very-similarly-named mpfrc++. The steps that worked for me are:

1. Install gmp and mpfr via homebrew

2. Download and unzip "mpfrc++-3.6.8.zip" from
   http://www.holoborodko.com/pavel/mpfr/#download

3. Copy the mpreal header file ("mpreal.h") to
   /usr/local/include (sudo cp ./mpreal.h /usr/local/include/) or, in your case, perhaps sudo cp ./mpreal.h /usr/local/opt/llvm/include would make more sense

4. Install/compile RcppMP
   (remotes::install_github("Thell/RcppMP",dependencies = TRUE))

I got some warnings but no errors, and the package loaded (library(RcppMP)), so I'm relatively confident it installed successfully. If you find otherwise, please let me know and I'll look into it further.

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