R - Install_Github Fails

Install with devtools::install_github() fails to detect build tools

Looks like there are a few issues that you need to overcome to install this package (xcode command line tools and OpenMP support for a start), but you should overcome them if you follow the instructions here: https://stackoverflow.com/a/65334247/12957340

After making the necessary changes, I successfully installed gsynth on my system (macOS Big Sur 11.2.3 / R version 4.0.3) using devtools::install_github('xuyiqing/gsynth') without issue.

--

Here are the instructions in case the link above dies:

1. Reinstall xcode command line tools (even if it says "up to date")

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 via Homebrew, skip to the next step

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

3. Once you 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/

# 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. Create a new ~/.R/Makevars file (if you already have a ~/.R/Makevars file, save it in a different directory (away from ~/.R/)) and include only these lines in the file:

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

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

7. If your package fails to compile, a couple of SO users have had to install a fresh gfortran (re: https://stackoverflow.com/a/65334247/12957340), which you can download from https://github.com/fxcoudert/gfortran-for-macOS/releases/tag/10.2-bigsur-intel

devtools install_github fails

The issue has been fixed like this which also worked for me according to: https://github.com/r-lib/devtools/issues/1978

• Run devtools::install_github("r-lib/remotes")
• Restart R.
• Run devtools::install_github("...") for the intended package.

R Unable to Install Packages From GitHub (System Error 267 @win/processx.c:1040)

The standalone mode of the remotes package solved the issue for me,
as suggested by the maintainer of processx (Gábor Csárdi) here

devtools::install_github() only calls remotes::install_github().

However, for the remotes, there is the option to be exectued in standalone mode

Source: Cran

Standalone mode

remotes will use the curl, git2r and pkgbuild packages if they are
installed to provide faster implementations for some aspects of the
install process. However if you are using remotes to install or update
these packages (or their reverse dependencies) using them during
installation may fail (particularly on Windows).

If you set the environment variable R_REMOTES_STANDALONE="true" (e.g.
in R Sys.setenv(R_REMOTES_STANDALONE="true")) you can force remotes to
operate in standalone mode and use only its internal R
implementations. This will allow successful installation of these
packages

With the following lines of code, gt was finally successfull installed from github.

Sys.setenv(R_REMOTES_STANDALONE="true")
remotes::install_github("rstudio/gt")

Thanks all the commentators for your help!

Update October / 2021

To avoid having to do these steps (Set in standanlone mode, and install with remotes) over and over again everytime you want to install a new package from github another convenient workaround is to just rollback to the previous version of processx as adviced by @rempsy in the github issue:

install.packages("pacman")
pacman::p_del(processx)
# Installing previous verison 3.5.1
install.packages("https://cran.r-project.org/src/contrib/Archive/processx/processx_3.5.1.tar.gz", repos=NULL, type="source") 

After the rollback of processx to version 3.5.1, devtools::install_github() works as expected, e.g.

devtools::install_github("rstudio/gt")

---

Related Topics