clang-7:错误:链接器命令失败，macOS大Sur的退出代码1失败

Question

安装需要在macOS中编译的R软件包自Big以来就中断了。这里就是这样一个例子。

> install.packages('nlme')

  There is a binary version available but the source version is later:
      binary  source needs_compilation
nlme 3.1-150 3.1-151              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘nlme’

trying URL 'https://cran.rstudio.com/src/contrib/nlme_3.1-151.tar.gz'
Content type 'application/x-gzip' length 805592 bytes (786 KB)
==================================================
downloaded 786 KB

* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
"gfortran-4.8" -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c chol.f -o chol.o
gfortran-4.8: warning: couldn’t understand kern.osversion ‘20.1.0
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c corStruct.c -o corStruct.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c gnls.c -o gnls.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix.c -o matrix.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nlOptimizer.c -o nlOptimizer.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nlme.c -o nlme.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c nlmefit.c -o nlmefit.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pdMat.c -o pdMat.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pythag.c -o pythag.o
"gfortran-4.8" -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c rs.f -o rs.o
gfortran-4.8: warning: couldn’t understand kern.osversion ‘20.1.0
clang -mmacosx-version-min=10.13 -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 nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: framework not found CoreFoundation
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [nlme.so] Error 1
ERROR: compilation failed for package ‘nlme’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/nlme’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/nlme’
Warning in install.packages :
  installation of package ‘nlme’ had non-zero exit status

The downloaded source packages are in
    ‘/private/var/folders/_3/b8whcf8d1bb8w_lr2rrscb5m0000gp/T/RtmpWCjwfs/downloaded_packages’

我尝试过重新安装xcode和命令行工具，并完成了Brew更新+升级。如有任何建议请见谅。

Answer 1

这一直具有挑战性，但下面是我从MacOS Big上的源代码编译R包的步骤：

1. 重新安装xcode命令行工具

(不要相信软件更新，如果它说‘最新’-他说谎- brew doctor说我的版本实际上是旧的)

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

1. 通过安装Homebrew的说明安装gcc & llvm，或者，如果已经安装gcc/llvm，跳到下一步

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

1. 如果您已经通过国产安装了gcc & llvm：

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

1. 将一些标头链接到/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

1. 编辑您的~/.R/Makevars文件(如果在您的~/.R/目录中没有一个名为Makevars的文件，请创建它)，并只包括以下几行：

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

1. 在R/Rstudio中从源代码编译包

# 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")

更新(2022/04/05)

更新"RcppAlgos“时出错(找不到gmp.h或libgmp)。我检查了gmp是否已安装(brew install gmp)，然后将/usr/local/include添加到CPPFLAGS，并在~/.R/Makevars文件中向LDFLAGS添加/usr/local/lib，以解决问题，即

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++