R 4.6 is Available

software
update
r
Author

Henrik Bengtsson

Published

July 26, 2026

The R Logo

TL;DR

R 4.6.0 was released on 2026-04-24 and R 4.6.1 on 2026-06-24. Both are now available on Wynton through the CBI software stack. I have validated that almost all CRAN and Bioconductor packages can be installed with this new version.

Using R

To use the latest R 4.6, which is the new default version, load it as:

{alice@dev3 ~}$ module load CBI r

Then you can run R interactively from the terminal using:

{alice@dev3 ~}$ R --quiet
> getRversion()
[1] '4.6.1'

To use R 4.6 in RStudio, just follow our RStudio documentation.

R packages must be re-installed

As usual when we move to a new version (e.g. from R 4.5 to R 4.6), any R packages installed in the previous version (R 4.5) are not available in the new version (R 4.6). This is not the case when we move from one patch version to another, e.g. R 4.6.0 to R 4.6.1. With the release of R 4.6.0 we have to start from scratch and reinstall any packages we need. So, don’t be surprised when library(futurize) gives an error on “there is no package called ‘futurize’”. Also, when installing your first package in a new version of R, R asks:

> install.packages("futurize")
Warning in install.packages("futurize") :
  'lib = "/wynton/home/cbi/shared/software/_rocky8/R-4.6.1-gcc13/lib64/R/library"'
  is not writable
Would you like to use a personal library instead? (yes/No/cancel)

Answer yes to this and anything else that R asks you to confirm. Doing so will make sure you get a smooth ride when using R. This is all explained in our R documentation.

Installation has been well validated

Just as with previous versions of R available via the CBI stack, I have validated that nearly all R packages on CRAN and Bioconductor can be installed out of the box using the R 4.6.1 installation.

I have confirmed that 24,348 (99.8%) out of 24,3941 CRAN packages and 2,379 (99.8%) out of 2,3842 Bioconductor 3.23 (2026-04-29) software3 packages are straightforward to install4. A small number of packages required some extra love - see our R documentation for guidance on installing those.

The 46 CRAN and 5 Bioconductor software packages that failed to install5 do so either because they depend on a system library that is not available on the cluster, or because they have bugs preventing them from being installed out of the box.

A nice side effect of this validation round is that it identified several third-party tools and libraries that were either missing or outdated on the cluster. As a result, a number of new CBI modules were added, and several existing ones were updated to more recent versions. This benefits everyone on Wynton, also those who do not use R.

Footnotes

  1. CRAN: nrow(available.packages(repos = "https://cran.r-project.org"))↩︎

  2. Bioconductor: nrow(available.packages(repos = "https://bioconductor.org/packages/3.23/bioc"))↩︎

  3. I only validated installation of Bioconductor “software” packages. There are also Bioconductor “annotation-data”, “experiment-data”, and “workflow” packages, which I assume will install out-of-the-box.↩︎

  4. The package installation checks took several days to complete.↩︎

  5. The CRAN packages that were not installed are: ‘bigrquerystorage’, ‘bizdays’, ‘blosc’, ‘cbbinom’, ‘chomper’, ‘CMCMC’, ‘cncaGUI’, ‘CVXR’, ‘designmatch’, ‘flint’, ‘fluidsynth’, ‘GeneralizedUmatrixGPU’, ‘geozarr’, ‘ggsql’, ‘GreedyExperimentalDesign’, ‘h5lite’, ‘hdf5lib’, ‘hypergeo2’, ‘minired’, ‘mos’, ‘multibridge’, ‘multiscape’, ‘myTAI’, ‘OpenCL’, ‘opencv’, ‘OptimalRerandExpDesigns’, ‘otinference’, ‘prioriactions’, ‘Rcplex’, ‘RcppMeCab’, ‘relations’, ‘rib’, ‘rip.opencv’, ‘RmecabKo’, ‘ROI.plugin.cplex’, ‘ROracle’, ‘roxigraph’, ‘Rpoppler’, ‘RQuantLib’, ‘Rtinycc’, ‘rzmq’, ‘sbw’, ‘sparsediff’, ‘sparselu’, ‘Uno’, and ‘zarr’. The Bioconductor software packages that were not installed are: ‘ChemmineOB’, ‘MsBackendRawFileReader’, ‘NewWave’, ‘rawrr’, and ‘SharedObject’.↩︎