feat: Speed up R builds #67

m1so · 2026-01-23T14:00:18Z

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 · 2026-01-23T14:00:35Z

📝 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 · 2026-01-23T14:04:57Z

ir/ir-with-libs/Dockerfile.ir

+RUN apt-get update \
+  && apt-get install -y ${BUILDDEPS} \
+  && R -e " \
+    options(Ncpus = 4); \
+    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/*


⚠️ Potential issue | 🔴 Critical

🧩 Analysis chain

🏁 Script executed:

# Find and read the Dockerfile find . -name "Dockerfile.ir" -path "*ir-with-libs*" | head -5

Repository: deepnote/environments

Length of output: 96

🏁 Script executed:

# Read the entire Dockerfile to understand the structure cat "ir/ir-with-libs/Dockerfile.ir"

Repository: deepnote/environments

Length of output: 1544

rJava will fail at runtime after BUILDDEPS is purged

rJava requires a Java runtime, but default-jdk (the only Java package installed) gets removed. Install default-jre-headless separately and only purge build dependencies.

🔧 Suggested 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); \ 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/*

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

RUN apt-get update \

&& apt-get install -y ${BUILDDEPS} \

&& R -e " \

options(Ncpus = 4); \

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/*

ENV RUNTIME_DEPS="default-jre-headless"

RUN apt-get update \

&& apt-get install -y ${RUNTIME_DEPS} ${BUILDDEPS} \

&& R -e " \

options(Ncpus = 4); \

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/*

🧰 Tools

🪛 Checkov (3.2.334)

[low] 1-78: Ensure that HEALTHCHECK instructions have been added to container images

(CKV_DOCKER_2)

[low] 1-78: Ensure that a user for the container has been created

(CKV_DOCKER_3)

🤖 Prompt for AI Agents

In `@ir/ir-with-libs/Dockerfile.ir` around lines 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.

I assume this bug must have been there forever as I didn't change the build logic, only refactored the RUN directives a bit

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash # Check the git history of the file to see the previous version git log --oneline -n 10 -- ir/ir-with-libs/Dockerfile.ir # Show the version before this PR git show HEAD:ir/ir-with-libs/Dockerfile.ir | grep -A 20 "apt-get remove"

Length of output: 487

@m1so You're right. The git history confirms apt-get remove --purge -y ${BUILDDEPS} was already there before your changes. Your refactoring consolidated the R package installation but didn't alter the cleanup logic.

Worth fixing now that it's surfaced though. Do you want to address it in this PR or track separately?

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/*

coderabbitai · 2026-01-23T15:02:25Z

ir/ir-with-libs/Dockerfile.ir

+# Use Posit Package Manager for precompiled Linux binaries
+ENV CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/bullseye/latest"
+


🧹 Nitpick | 🔵 Trivial

Pin CRAN snapshot for reproducible builds.
Using latest can shift binaries over time. Prefer a dated snapshot URL to keep images deterministic.

♻️ Example update

-ENV CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/bullseye/latest" +ENV CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/bullseye/2026-01-23"

📝 Committable suggestion

‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.

Suggested change

# Use Posit Package Manager for precompiled Linux binaries

ENV CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/bullseye/latest"

# Use Posit Package Manager for precompiled Linux binaries

ENV CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/bullseye/2026-01-23"

🤖 Prompt for AI Agents

In `@ir/ir-with-libs/Dockerfile.ir` around lines 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.

feat: Speed up R builds

a55fb39

coderabbitai bot requested changes Jan 23, 2026

View reviewed changes

fix: Add HTTPUserAgent to actually download precompiled packages

3f01a39

coderabbitai bot requested changes Jan 23, 2026

View reviewed changes

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feat: Speed up R builds #67

feat: Speed up R builds #67

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		# Use Posit Package Manager for precompiled Linux binaries
		ENV CRAN_REPO="https://packagemanager.posit.co/cran/__linux__/bullseye/latest"

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