check_build_tools error in macOS 13.1, Xcode 14.2

[mbac]

Hi,

I just updated both macOS and Xcode and I'm getting the following:

> pkgbuild::check_build_tools(debug = TRUE)
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/usr/local/include   -fPIC  -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c foo.c -o foo.o
<built-in>: error: unknown value ‘13.1.0’ of ‘-mmacosx-version-min’
make: *** [foo.o] Error 1
Error: Could not find tools necessary to compile a package
Call `pkgbuild::check_build_tools(debug = TRUE)` to diagnose the problem.

Not sure this is an issue with the package or my system, but I noticed error: unknown value ‘13.1.0’ of ‘-mmacosx-version-min’.

pkgbuild version is 1.4.0 running in R 4.2.2. Command line tools have been installed via brew in /Library/Developer/CommandLineTools.

Running the above also triggers Rstudio's Xcode command line tools installation GUI, but even if I click Ok nothing happens.

Thanks, —M

[gaborcsardi]

That looks like a mis-configured system to me, I don't think R should call /usr/local/gfortran/bin/gcc. This is how this looks like on my system:

❯ pkgbuild::check_build_tools(debug = TRUE)
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/bin/R \
  CMD SHLIB foo.c
clang -arch arm64 -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib -L/opt/R/arm64/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/Versions/4.2-arm64 -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups

and for intel:

❯ pkgbuild::check_build_tools(debug = TRUE)
Trying to compile a simple C file
Running /Library/Frameworks/R.framework/Versions/4.2/Resources/bin/R CMD \
  SHLIB foo.c
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Versions/4.2/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c foo.c -o foo.o
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/Versions/4.2/Resources/lib -L/usr/local/lib -o foo.so foo.o -F/Library/Frameworks/R.framework/Versions/4.2 -framework R -Wl,-framework -Wl,CoreFoundation

Check if you set PATH to /usr/local/gfortran/bin, or if you change the compiler paths in .Renviron, etc.

[mbac]

Hi,

I just re-installed everything and deleted .Renviron and .Rprofile where they could be found. Something is still telling R to call gcc in that directory but if I run which gcc I get /usr/bin/gcc, which is not a link to that other version.

The "gfortran" version was installed by homebrew when I used that compiler to work around some other error I was having. I have uninstalled /usr/local/gfortran/bin/gcc but R is still calling that file when I run check_build_tools(debug = TRUE). The error message stays the same.

I would be grateful if you could suggest where else to check as to why R keeps wanting to use that version of gcc.

PS: /usr/local/gfortran/bin is not in PATH

[gaborcsardi]

How did you install R? What does R CMD config CC say? What does system("R CMD config CC") say from R?

[mbac]

They both report: /usr/local/gfortran/bin/gcc -fopenmp … but I just reinstalled R from the latest CRAN binary, after uninstalling it with their suggested command

sudo rm -Rf /Library/Frameworks/R.framework /Applications/R.app \
   /usr/local/bin/R /usr/local/bin/Rscript

[gaborcsardi]

Do you have something in ~/.R/Makevars?

[mbac]

I guess you found it:

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,-L/usr/local/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/usr/local/include

I guess this was added when I had to resort to the Homebrew compiler. If I delete it will R just revert to defaults?

Thanks again…

[gaborcsardi]

If I delete it will R just revert to defaults?

Yes.

[mbac]

Worked fine. Thanks a lot, and sorry for barking up the wrong tree 🙂