feat: Speed up R builds

[m1so]

Summary by CodeRabbit

• Chores
  • Switched R package installs to the Posit Package Manager CRAN mirror for faster, more reliable binary installs (including IR kernel setup).
  • Consolidated per-package R installs into a single, parameterized bulk installation and simplified OS package flow to streamline builds and improve maintainability.

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[coderabbitai]

📝 Walkthrough

Walkthrough

Two Dockerfiles updated to change how R packages are installed. ir/ir-base/Dockerfile.ir now installs IRkernel from the Posit Package Manager CRAN mirror and calls IRkernel::installspec(). ir/ir-with-libs/Dockerfile.ir replaces many per-package R install commands with environment variables CRAN_REPO and R_PACKAGES and a single R -e invocation to install all packages, and consolidates apt-get into a single update/install/clean sequence while removing explicit per-package installation blocks.

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'Speed up R builds' directly matches the main changes: both Dockerfiles now use Posit Package Manager for faster installations.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.

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[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@ir/ir-with-libs/Dockerfile.ir`:
- Around line 66-78: The Dockerfile removes Java runtime when purging
${BUILDDEPS}, breaking rJava at runtime; ensure a JRE package remains by
installing default-jre-headless separately and not removing it: add
default-jre-headless to the apt-get install step (outside of ${BUILDDEPS}) or
install it in the same RUN before the apt-get remove --purge -y ${BUILDDEPS}
line, and keep the apt-get remove call targeting only ${BUILDDEPS} so
default-jre-headless (needed by rJava) is preserved.

[coderabbitai]

Actionable comments posted: 1

🤖 Fix all issues with AI agents

In `@ir/ir-with-libs/Dockerfile.ir`:
- Around line 50-52: The CRAN repo is set to a moving "latest" snapshot via the
ENV CRAN_REPO variable; replace that value with a dated Posit Package Manager
snapshot URL to pin binaries for reproducible builds (update the ENV CRAN_REPO
entry in Dockerfile.ir to a specific snapshot date, e.g. use the Posit snapshot
path with a YYYY-MM-DD segment instead of "latest"). Ensure the ENV CRAN_REPO
assignment is updated wherever it appears so builds use the fixed dated
snapshot.

♻️ Duplicate comments (1)

ir/ir-with-libs/Dockerfile.ir (1)

66-81: rJava will miss a runtime Java after purge.
default-jdk is removed with ${BUILDDEPS}, leaving no JRE for rJava. Keep a runtime JRE outside the purge.

🔧 Minimal fix

+ENV RUNTIME_DEPS="default-jre-headless"
 RUN apt-get update \
-  && apt-get install -y ${BUILDDEPS} \
+  && apt-get install -y ${RUNTIME_DEPS} ${BUILDDEPS} \
   && R -e " \
     options( \
       Ncpus = 4, \
       HTTPUserAgent = sprintf('R/%s R (%s)', getRversion(), paste(getRversion(), R.version['platform'], R.version['arch'], R.version['os'])) \
     ); \
     install.packages( \
       strsplit(Sys.getenv('R_PACKAGES'), '\\\\s+')[[1]], \
       repos = Sys.getenv('CRAN_REPO'), \
       dependencies = TRUE \
     ) \
   " \
   && apt-get clean \
   && apt-get remove --purge -y ${BUILDDEPS} \
   && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*