Howto: UCRT3 and testing new Rtools for Windows

Tomas Kalibera

The download locations for Rtools are available from as usual. This now relates only to the development of new Rtools version.


This document is now only about a system for testing updates to Rtools on Windows. It is intended for Rtools maintainers, could be of interest to people automating R package checks or R enthusiasts at large, but is not of general interest to R users nor R package authors.

Evolution of ucrt3 and this document

This document was once named “Howto: UTF-8 as native encoding in R on Windows with UCRT”.

The ucrt3 system was created to enable the transition to UTF-8 as the native encoding in R on Windows, which required switching to UCRT as the C runtime, a new toolchain, and updates to R and R packages. This document provided instructions on how to build the experimental versions of R and R packages, how to update R packages to be compatible, how to build the new toolchain and how to contribute to it.

From March, 2021, the system implemented automated builds and testing. Usually several times a week it would provide builds of the new toolchain, a patched version of R-devel, patched versions of CRAN and required Bioconductor packages, and checks of CRAN packages. The check results were integrated into CRAN website, so available for each CRAN package. Later this involved also regular builds of the Rtools installer.

From December 13, 2021, R-devel has been switched to UCRT on Windows. The ucrt3 patches for R were merged into R-devel and the CRAN checks of R-devel were switched to the new toolchain, Rtools42. From this time, this document was used by package authors who needed to change their R packages to work on Windows and the ucrt3 system was still running as an alternative to the main CRAN checks. It has been still used to build new versions of Rtools42 and R-devel snapshots and it served R (CRAN and Bioconductor) package patches that were installed automatically at package installation time by R-devel.

In March, 2022, the automated patching of R packages in R-devel was disabled. This document was transformed into Howto: Building R 4.2 and packages on Windows, which is an external documentation linked to the R 4.2 release and a similar document was started for R-devel, to eventually include specifics of the new development version of R. The CRAN/R-project website now contains R builds (R 4.2, R-devel) using Rtools42. The automated checks ran by ucrt3 system were removed from the CRAN website. The ucrt3 system may again diverge from R-devel and may patch CRAN and Bioconductor packages when needed for testing new versions of Rtools and at this point package authors don’t have to worry about such differences.

This document is available in subversion as

One can use a subversion client to retrieve an older version.

The history of the transition is also covered by blog posts:

Why the system was created

For UTF-8 as native encoding on Windows, we needed a new compiler toolchain and we needed to rebuild all source code with it linked to R and to R packages (at least code linked to it statically, even though sometimes even code linked dynamically).

It was clear that a lot of code patching for this will be necessary (R and R packages use fixed Make files to link, R packaged used to download pre-compiled static libraries, major upgrades of GCC and MinGW-W64 were needed and it turn required patching).

Such changes had to be tested, by CRAN package checks, and it was clear that those checks would have to be ran repeatedly as the toolchain would grow and evolve. There was not a suitable system ready for re-use on Windows.

Key features

The system automates all steps from sources to package check results: building the toolchain and libraries, building the Tcl/Tk bundle, building an Rtools installer, building R and R installer, building binary versions of CRAN and needed Bioconductor R packages, running checks for those packages. The automation includes installation of external software on all systems, including software needed to run packages on Windows.

The system does not depend on external services. The sources are in subversion run by the R project. It is implemented in shell scripts, PowerShell, and R. Shell scripts are used for automation even on Windows (used with Msys2). Parts of it run on Linux and parts on Windows, using interactive docker containers for isolation and reproducibility. It is designed to run on a server with many cores (rather than parallizing across machines).

The system differs from “traditional” CRAN package checks in several ways.

It only runs full checks from scratch and tests binary builds of R and R packages. Every iteration builds the toolchain and libraries from sources, using it builds the Tcl/Tk bundle, using those it builds the R installer and Rtools installer. It installs R via the R installer and builds binary versions of R packages. It installs R packages from those binary versions and checks them.

As all the components are versioned in subversion, it flags the individual builds by the revisions used. From the name of a tarball/exe/zip file of an individual component, such as the R installer, one sees which revision number of the toolchain, of R, and of the automation scripts was used, so one can find the corresponding sources.

The system is optimized for checking toolchains. Instead of building all CRAN packages, it only builds those than need compilation (of C/Fortran/C++ code), so only those than need the toolchain. For other packages, it uses the official CRAN builds. This saves time and disk space. To allow easy testing of the built version of R, the system patches R so that the default contrib URLs for package installation starts with a URL for a special package repository with only the binary packages built by this system. So, R will use these in preference. To prevent accidental installation of possibly newer packages from the official CRAN repository, the system had a safeguard and could have again if needed (R packages built by the system got a special field into DESCRIPTION, and only packages with that field were allowed for installation). The system only builds and installs Bioconductor packages needed by any of the CRAN packages.

The system uses installation-time patching of packages, which is now part of R, but not enabled in the released versions (nor in R-devel at the time of writing). There is a web repository, synced from subversion, which contains patches for R packages, indexed simply by package name, and split for CRAN and Bioconductor. These patches are automatically applied when the binary packages are built and the patches are added to the builds for transparency. The patches are synced to the web together with the binary builds. The patching allows to experiment with changes to the toolchain that would otherwise require package changes (but then it would no longer really be an experiment). Also, with a change that requires re-building of all packages, it would be impossible to wait for individual package authors to do the updates (with transition to UCRT, over 100 packages had to be patched, but many thousands of packages depended on them).


See subversion for the source code of the system and see comments in the files.

toolchain_libs is to build the toolchain and libraries. It is to be run on a Linux machine or on any machine that can run Linux docker containers. As in the following, there is a script which runs a build iteration in a docker container. If the container doesn’t exist, it is created and all software needed there is installed, but if it already exists, it is re-used including partially re-using the build. The container is stopped by the script at exit and it can be explored later from the command line (but the main log files are copied out of the container automatically). The toolchain and libraries are built using MXE (with some updates), which is included in the source tree.

tcl_bundle builds the Tcl/Tk bundle using the toolchain. It is to be run on a Linux machine or on any machine that can run Linux containers.

rtools builds the Rtools installer from the toolchain and libraries provided above, adding Msys2 as build tools. This and all other components built on Windows requires Msys2 (as it is implemented in Unix shell). The rtools installer is build in a docker container, which has its own installation of Msys2 (docker here is used to separate two possibly incompatible Cygwin runtimes, in addition to reproducibility). This has to be run on Windows because only Windows can run Windows docker containers.

r builds R and R installer. This is run on Windows in a Windows docker container. There are .ps1 scripts to install external software needed to build R. These scripts re-use installers of such software if already available to prevent excessive downloads on every new run (but as other containers used in the system, repeated runs normally re-use the containers; the containers only need to be dropped manually when the set of software to be installed there changes).

r_packages has scripts to build binary versions of R packages (in a Windows docker container) and to check all packages (in another Windows docker container). There are also scripts for checking a single package (in yet another docker container) with prepared support for on-demand checking, but that is not regularly used. There is a .ps1 script to install external software needed for checking (installed inside the container).

Web repository

There is a web repository of builds produced by runs of this system, including builds of Rtools, the Tcl/Tk bundle, R-devel snapshots, R-patched snapshots, Rtools installer, CRAN and Bioconductor binary packages (subsets of), patches of the packages and check results for CRAN packages. These files are created by these scripts with more details in the scripts.

Please note these are not official builds for use, they are only for experimentation.

These are experimental builds and may differ from R-devel, may have the patched packages, may have not yet well tested Rtools, may use different version of Rtools from the one officially for that release of R, may be very unstable.

Otherwise, as of now, the builds can be used for experimentation the same way as Howto: Building R-devel and packages on Windows describes. The names of the components are slightly different and are expected to change over time, but are similar to those in Rtools42 and are documented in the individual scripts.