feat(upgrade): bi-annual RStudio package update

[andyatmiami]

Description

This commit is related to the ongoing work to release the 2025a software upgrade.

Upgrades:

• R
  • 4.4.1 -> 4.4.3
• RStudio
  • rstudio-server-rhel-2024.04.2-764-x86_64.rpm -> rstudio-server-rhel-2024.12.1-563-x86_64.rpm
• tidymodels
  • 1.2.0 -> 1.3.0
• plumber
  • 1.2.2 -> 1.3.0

A couple other "quality of life" improvements were included:

• Refactored Dockerfile to combine RUN statements where obvious/low-risk
• Better use of ARG references to reduce copy-pasta in Dockerfile instructions
• install_packages.R script externalizes the userland software installs in an external script to better "share" across cpu + cuda Dockerfile variants
• Fixed issue(s) with kustomize cuda overlay so now kubectl apply -k overlays/accelerator/cuda works

Related-to: https://issues.redhat.com/browse/RHOAIENG-19484

How Has This Been Tested?

Verification was performed in the following manner:

1. [CUDA only] Acquire a CUDA-enabled ROSA cluster
   • https://docs.google.com/document/d/1OZ7vJnUg_3ei6Unb8pyPSAuYJtWQykMWgoXd2EocslA/edit?tab=t.0#heading=h.i94r0gk7mutm
2. All relevant RStudio images built locally
3. [CUDA only] Kustomize manifests used in testing updated
   • nodeSelector added to ensure workload deployed on worker node with GPU
   • resources adjusted to provide more memory and also to request GPU
   • emptyDir volume added to mimic production usage
     • was getting Permission Denied errors related to /opt/app-root/src/.cache
4. deploy% target of Makefile used to deploy image
5. ``validate%` target used to run tests and confirmed all tests succeeded
6. undeploy% target of Makefile used to undeploy image / prepare environment for next image

Simply to better equate myself with R - I also ran this simple script within the pod to confirm versions of dependencies installed:

(app-root) bash-5.1$ cat test_versions.R

# test_versions.R

# List of packages to check
packages <- c("Rcpp", "tidyverse", "tidymodels", "plumber", "vetiver", "devtools")

# Loop through each package in the list
for (package_name in packages) {
  # Check if the package is installed
  if (requireNamespace(package_name, quietly = TRUE)) {
    # Retrieve and print the version of the installed package
    package_version <- packageVersion(package_name)
    cat(sprintf("The installed version of '%s' is: %s\n", package_name, package_version))
  } else {
    cat(sprintf("The package '%s' is not installed.\n", package_name))
  }
}

(app-root) bash-5.1$ Rscript test_versions.R

The installed version of 'Rcpp' is: 1.0.14
The installed version of 'tidyverse' is: 2.0.0
The installed version of 'tidymodels' is: 1.3.0
The installed version of 'plumber' is: 1.3.0
The installed version of 'vetiver' is: 0.2.5
The installed version of 'devtools' is: 2.4.5

Merge criteria:

• The commits are squashed in a cohesive manner and have meaningful messages.
• Testing instructions have been added in the PR body (for PRs involving changes that are not immediately obvious).
• The developer has manually tested the changes and verified that the changes work

[openshift-ci]

Skipping CI for Draft Pull Request.
If you want CI signal for your change, please convert it to an actual PR.
You can still manually trigger a test run with /test all

[atheo89]

Thanks Andy, added only a question, apart of this /lgtm

[andyatmiami]

/override "ci/prow/images" "ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror"

more examples of https://issues.redhat.com/browse/OCPBUGS-50507 that continues to plague us 😢

[openshift-ci]

@andyatmiami: Overrode contexts on behalf of andyatmiami: ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror, ci/prow/images

In response to this:

/override "ci/prow/images" "ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror"

more examples of https://issues.redhat.com/browse/OCPBUGS-50507 that continues to plague us 😢

Instructions for interacting with me using PR comments are available here. If you have questions or suggestions related to my behavior, please file an issue against the kubernetes-sigs/prow repository.

[harshad16]

/lgtm

imported in cluster: ✔️

[jiridanek]

/lgtm
/approve

[openshift-ci]

[APPROVALNOTIFIER] This PR is APPROVED

This pull-request has been approved by: jiridanek

The full list of commands accepted by this bot can be found here.

The pull request process is described here

Needs approval from an approver in each of these files:

• OWNERS [jiridanek]

Approvers can indicate their approval by writing /approve in a comment
Approvers can cancel approval by writing /approve cancel in a comment

[atheo89]

/override ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror

[openshift-ci]

@atheo89: Overrode contexts on behalf of atheo89: ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror

In response to this:

/override ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror

Instructions for interacting with me using PR comments are available here. If you have questions or suggestions related to my behavior, please file an issue against the kubernetes-sigs/prow repository.

[atheo89]

/override "ci/prow/images" "ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror" "ci/prow/rstudio-notebook-e2e-tests"

[openshift-ci]

@atheo89: Overrode contexts on behalf of atheo89: ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror, ci/prow/images, ci/prow/rstudio-notebook-e2e-tests

In response to this:

/override "ci/prow/images" "ci/prow/cuda-rstudio-c9s-python-3-11-pr-image-mirror" "ci/prow/rstudio-notebook-e2e-tests"

Instructions for interacting with me using PR comments are available here. If you have questions or suggestions related to my behavior, please file an issue against the kubernetes-sigs/prow repository.

[atheo89]

/override "ci/prow/rstudio-c9s-python-3-11-pr-image-mirror"

[openshift-ci]

@atheo89: Overrode contexts on behalf of atheo89: ci/prow/rstudio-c9s-python-3-11-pr-image-mirror

In response to this:

/override "ci/prow/rstudio-c9s-python-3-11-pr-image-mirror"

Instructions for interacting with me using PR comments are available here. If you have questions or suggestions related to my behavior, please file an issue against the kubernetes-sigs/prow repository.