Rtools 40

New experimantal toolchain for R on Windows based on gcc 8 and msys2.

Install Rtools40 and R-testing

Rtools40 does not conflict with other versions of Rtools and can be installed alongside existing Rtools 3.5 installations.

The daily build of R-testing is a modified version of R-devel configured for the new toolchain.

For now, R-testing automatically sets the PATH in R to use make and gcc from rtools40. No need to modify the Windows system PATH. This is a temporary solution to run R-testing alongside R 3.5.1. Make sure you do not override the PATH in your ~/.Renviron file.

Help and Reporting Problems

If you find a problem in a package or cannot make it work, open a ticket here: https://github.com/r-windows/checks/issues. Only report issues here that are specific to the new Rtools toolchain. Check that:

  • The problem does not pre-exist on the CRAN with the current Windows toolchain
  • The error/warning does not appear with GCC-8 on Fedora/Debian on CRAN
  • One issue per package

Please be patient, a toolchain upgrade with 12k packages is a complex operation.

System Software

Because CRAN does not provide binaries for the new toolchain yet, R-testing installs all packages from source.

Some R packages require external libraries or software to build. Rtools40 includes a package manager which you can use to install additional rtools packages. There should be a shortcut to the Rtools terminal in your Start Menu.

The package mananger is called pacman: the native package manager from arch linux which has been ported to Windows by msys2.

# Update repo index
pacman -Sy

Binary packages are prefixed with mingw-w64-686- for the win32 version and with mingw-w64-x86_64- for the win64 build. To build an R package we typically need both, for example to install the coinor library:

# Install libcurl
pacman -S  mingw-w64-{i686,x86_64}-coinor

Now we can install the R package. Rtools will automatically find libraries installed by pacman, no need to set custom paths.

# Run in R:
install.packages("Rsymphony")

Compiling R Packages with Custom Flags

Some older R packages do not use the correct flags by default and need a little help. You can pass additional compiler and linker flags by setting these environment variables:

  • LOCAL_CPPFLAGS: custom C/C++ flags passed when compiling
  • LOCAL_LIBS: custom flags when linking

An example is the old XML package. First install libxml2 in rtools:

# Run this in Rtools
pacman -S mingw-w64-{i686,x86_64}-libxml2

And then install XML like this:

# Run this in R
Sys.setenv(LOCAL_CPPFLAGS = "-I/mingw$(WIN)/include/libxml2")
Sys.setenv(LOCAL_LIBS = '-llzma')
install.packages("XML")

Managing System Packages

First update the repository list:

# Update repo index
pacman -Sy

# Upgrade installed packages
pacman -Su

To list all rtools packages currently available:

pacman -Sl

Find out more at the pacman website.

Automated Installation

I run this every day on my build server to update and install all available rtools packages:

# Update all the packages!!
pacman -Syu --noconfirm
pacman -S --needed --noconfirm $(pacman -Slq | grep mingw-w64-)