[Bioc-devel] new Windows toolchain for R-3.3.0

Dan Tenenbaum dtenenba at fredhutch.org
Thu Mar 31 19:36:08 CEST 2016

Hello all,

R is planning to use a new Windows toolchain (known as Rtools33) for the soon-to-be-released R-3.3.0.
This toolchain will use gcc/g++ 4.9.3 (an upgrade from 4.6.3).

We expect CRAN packages for Windows using this toolchain in a few days. 
We are currently building the devel branch of Bioconductor using the new toolchain and expect the results later today.

What this means:

- If you are using R-3.3.0 on Windows, please update to a recent version from
  https://cran.r-project.org/bin/windows/base/rtest.html  .
  You should do a completely fresh install (i.e., don't keep packages from 
  a previous install around).
- Set it up to use the new toolchain as follows:

There is a binary incompatibility between packages built with the old toolchain and packages built with the new toolchain (IF the packages or their system dependencies contain C++ code or bindings). 

At the moment, windows packages are not available for Bioconductor's devel branch. When they become available, later today, they will be packages built with the new toolchain, and should only be used by a recent R-3.3.0 which has been configured to use the new toolchain. 

You also need to set up R to NOT install binary packages (the process for doing this is described at the link above) because the binary packages provided by CRAN at the moment were built with the old toolchain and are not compatible.

Package authors should read 


Which describes how to set up a windows machine to build R packages using the new toolchain. 
This page will change over time as we get more packages / system dependencies to build.

You can test your packages using this setup.
If you don't have physical access to a windows machine, you can download a virtual machine from Microsoft:


This mailing list (bioc-devel) is the appropriate place for questions about the new toolchain.

When the build report from today's build is available, I may send a follow-up email (either to bioc-devel or specific maintainers) to discuss how to get certain packages to install under the new toolchain.


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