Clang, make, and other Mac M1 installation errors

Hi there!

Since moving to an M1 Macbook Air last year, I've had all sorts of installation problems with R packages. A few months ago I went through some hair pulling, and I think I'm missing some basic information about how all this works.

I'll put more info below, but I'm hoping for your help (1) fixing the problem, and/or (2) finding some resources/readings to help me learn to fish when I have problems like this in the future.

Here's a recent problem--

I tried to install a bioconductor package, but failed to build some of its dependencies from source:

> BiocManager::install("GenomicRanges")
Installing package(s) 'GenomicRanges'
also installing the dependencies ‘zlibbioc’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘XVector’

Packages which are only available in source form, and may need compilation of C/C++/Fortran: ‘zlibbioc’ ‘S4Vectors’ ‘IRanges’ ‘XVector’
  ‘GenomicRanges’
Do you want to attempt to install these from sources? (Yes/no/cancel) 
[...]
* installing *source* package ‘zlibbioc’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make: brew: Command not found
make: brew: Command not found
make: brew: Command not found
make: brew: Command not found
mkdir -p "/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/00LOCK-zlibbioc/00new/zlibbioc/include"
/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I"/include" -I"/include" -I"/include" -isysroot "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" -Xclang -fopenmp   -fPIC  -g -O2 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c R_init_zlibbioc.c -o R_init_zlibbioc.o
/bin/sh: /bin/clang: No such file or directory
make: *** [R_init_zlibbioc.o] Error 127
ERROR: compilation failed for package ‘zlibbioc’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/zlibbioc’

I see variations on this general error pattern a lot and have brew installed. A while back to fix a problem like this, I followed a GitHub issue and edited my Makevars to look like this:

julian (-bash) :~$ cat ~/.R/Makevars
XC_LOC:=$(shell xcrun --show-sdk-path)
LLVM_LOC:=$(shell brew --prefix llvm)
GCC_LOC:=$(shell brew --prefix gcc)
GETTEXT_LOC:=$(shell brew --prefix gettext)
OMP_LOC:=$(shell brew --prefix libomp)

CC=$(LLVM_LOC)/bin/clang
CXX=$(LLVM_LOC)/bin/clang++
CXX11=$(LLVM_LOC)/bin/clang++
CXX14=$(LLVM_LOC)/bin/clang++
CXX17=$(LLVM_LOC)/bin/clang++
CXX1X=$(LLVM_LOC)/bin/clang++

CFLAGS=-g -O2 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O2 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L"$(LLVM_LOC)/lib" -L"$(GETTEXT_LOC)/lib" -Wl,-rpath,$(LLVM_LOC)/lib --sysroot="$(XC_LOC)" -lomp
CPPFLAGS=-I"$(GETTEXT_LOC)/include" -I"$(LLVM_LOC)/include" -I"$(OMP_LOC)/include" -isysroot "$(XC_LOC)" -Xclang -fopenmp

FC=$(GCC_LOC)/bin/gfortran
F77=$(GCC_LOC)/bin/gfortran
FLIBS=-L$(GCC_LOC)/lib/gcc/10/ -lm

And for reference:

julian (-bash) :~$ brew --prefix llvm
/opt/homebrew/opt/llvm
julian (-bash) :~$ /opt/homebrew/opt/llvm/bin/clang --help | head -2
OVERVIEW: clang LLVM compiler

And my sessionInfo:

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.0.1

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] BiocManager_1.30.16 compiler_4.1.1      prettyunits_1.1.1   remotes_2.4.2       tools_4.1.1         testthat_3.1.2      digest_0.6.29      
 [8] pkgbuild_1.3.1      pkgload_1.2.4       evaluate_0.15       memoise_2.0.1       lifecycle_1.0.1     gtable_0.3.0        rlang_1.0.2        
[15] cli_3.2.0           rstudioapi_0.13     curl_4.3.2          yaml_2.3.5          xfun_0.30           fastmap_1.1.0       gridExtra_2.3      
[22] withr_2.5.0         knitr_1.37          desc_1.4.1          fs_1.5.2            devtools_2.4.3      rprojroot_2.0.2     grid_4.1.1         
[29] glue_1.6.2          R6_2.5.1            processx_3.5.2      rmarkdown_2.13      sessioninfo_1.2.2   callr_3.7.0         purrr_0.3.4        
[36] magrittr_2.0.2      ps_1.6.0            ellipsis_0.3.2      htmltools_0.5.2     usethis_2.1.5       cachem_1.0.6        crayon_1.5.0  

Update: Here's the best resource I've found so far: Transitioning from x86 to arm64 on macOS - experiences of an R user

1 Like

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.