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UPDATING.md

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Updating didehpc for new R versions

Three steps are required. This document uses the addition of R 3.6.0 as an example, where the previous latest install was R 3.5.0.

Install the new version of R on all cluster nodes

  • Look in \\fi--didef3\Software\HPC\R.
  • Download the new R installer, and save it in the folder.
  • Install it locally. Verify the executable folders created are of this form:
    • C:\Program Files\R\R-3.6.0\bin\i386\Rscript.exe
    • C:\Program Files\R\R-3.6.0\bin\x64\Rscript.exe
  • Copy the most recent setr32_3_5_0.bat and setr64_3_5_0.bat to new filenames matching the new version.
  • Edit each one, so that the directories match the above - for example:
set path=%path%;C:\Program Files\R\R-3.6.0\bin\x64
  • Copy the most recent install file (eg, install_r_3_5.0.bat) to the new version name (install_r_3_6_0.bat).
  • Edit it, and change the version variable to match the new version:
set R_VERSION=3.6.0
  • Test the install manually on a single node by remote desktop.
  • If all seems well, use HPC Cluster Manager to install it on the nodes. I recommend no more than 30 at a time.
  • Update update_r_all.bat - add the new install batch file to the list, which gets used when installing a new node.

Update the package

  • On a new branch, update R/config.R
  • Update this block of code in the function rtools_versions, which associates the right version of Rtools with the right version of R. Verify this is the correct version of Rtools here.
  ret <- switch(r_version_2,
                "3.2" = list(path = "Rtools33", gcc = "gcc-4.6.3"),
                "3.3" = list(path = "Rtools33", gcc = "gcc-4.6.3"),
                "3.4" = list(path = "Rtools34", gcc = mingw),
                "3.5" = list(path = "Rtools34", gcc = mingw),
                "3.6" = list(path = "Rtools34", gcc = mingw),
                stop("Get Rich to upgrade Rtools"))
  • Locate the r_versions function and update the list of valid versions with the new one. This should match the filenames of the new setr32 and setr64 batch files created earlier.
r_versions <- function() {
  v <- c("3.2.2", "3.2.4", "3.3.1", "3.3.2", "3.4.0", "3.4.2", "3.4.4",
         "3.5.0", "3.6.0")
  • Update the minor version in DESCRIPTION, and add an entry in NEWS.md.
  • Commit changes on the branch - but wait for last step before PR / merging.

Update the bootstrap

Log into a remote desktop

remotes::install_github("mrc-ide/conan@prototype", upgrade = FALSE)

r_version <- paste(getRversion()[1, 1:2], collapse = ".")
path <- file.path("T:/conan/bootstrap", r_version)
conan::conan_bootstrap(path, TRUE)

Run this from both 4.0 and 3.6; we'll want to do this periodically.

The didehpc-pkgs should also be updated as that is where provisioning comes from (here to avoid conflicting package versions)

Finalising

  • Make a pull Request for the new version of didehpc, request a review, and await merging.
  • After merging, drat will need updating.
  • Inform Cluster channel on Teams