Add devcontainer configuration excluding rJava #97

google-labs-jules · 2026-01-11T23:25:34Z

This PR adds a .devcontainer configuration to the project. It sets up a development environment based on mcr.microsoft.com/devcontainers/r:latest.

Key features:

Java-Free Environment: The container is configured to start without Java. The dependency installation script (.devcontainer/setup.R) reads DESCRIPTION and installs all dependencies except rJava. This allows testing the package's functionality for downloading and installing Java.
Tooling:
- Installs Posit Air CLI for code formatting.
- Installs VS Code extensions: Posit.air-vscode and quarto.quarto.
Automation: The postCreateCommand runs a setup script that installs the Air CLI and the R dependencies.

PR created automatically by Jules for task 15392296075773728410 started by @e-kotov

- Use `mcr.microsoft.com/devcontainers/r:latest` as base image. - Exclude `rJava` from dependency installation to keep container Java-free. - Install Posit Air CLI and VS Code extension. - Install Quarto extension.

google-labs-jules · 2026-01-11T23:25:35Z

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codecov · 2026-01-11T23:28:37Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.80%. Comparing base (cbc4a78) to head (7d1190c).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #97   +/-   ##
=======================================
  Coverage   86.80%   86.80%           
=======================================
  Files          20       20           
  Lines        1993     1993           
=======================================
  Hits         1730     1730           
  Misses        263      263

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Copilot

Pull request overview

This PR adds a devcontainer configuration to facilitate development and testing of the rJavaEnv package in an environment without Java pre-installed. This is valuable for testing the package's core functionality of downloading and installing Java.

Changes:

Added devcontainer configuration using Microsoft's R devcontainer base image
Created setup scripts to install Posit Air CLI and R dependencies while explicitly excluding rJava
Configured VS Code extensions for R, Quarto, and Posit Air development

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 5 comments.

File	Description
`.devcontainer/devcontainer.json`	Defines the devcontainer configuration with base image, VS Code extensions, and post-create command
`.devcontainer/setup.sh`	Bash script that installs Posit Air CLI and executes R dependency setup
`.devcontainer/setup.R`	R script that reads DESCRIPTION and installs all dependencies except rJava

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Copilot · 2026-01-11T23:29:39Z

.devcontainer/setup.sh

+
+# Install Posit Air CLI
+echo "Installing Posit Air CLI..."
+curl -LsSf https://github.com/posit-dev/air/releases/latest/download/air-installer.sh | sh


The setup script should check if the Air CLI installation was successful before proceeding with R dependency installation. Consider adding a verification step after the curl command to ensure the installation didn't fail silently.

Copilot · 2026-01-11T23:29:39Z

.devcontainer/setup.R

+# Get dependencies from DESCRIPTION in the current directory
+deps <- remotes::dev_package_deps(dependencies = TRUE)
+
+# Filter out rJava to ensure no Java is installed
+packages_to_install <- deps$package[deps$package != "rJava"]
+
+# Install/Update the selected packages
+if (length(packages_to_install) > 0) {
+  # We use install_cran to handle versions if specified in DESCRIPTION (though usually remotes::install_deps does this better)
+  # But since we need to exclude one, we pass the vector.
+  # remotes::install_cran will install the latest CRAN version.
+  # To respect version requirements in DESCRIPTION, strictly speaking we should use something more sophisticated,
+  # but for a dev container, latest versions of dependencies are usually desired.
+  remotes::install_cran(packages_to_install)
+}


The script uses remotes::install_cran() which ignores version constraints specified in DESCRIPTION. This could lead to compatibility issues if the DESCRIPTION file specifies minimum versions for dependencies. Consider using remotes::install_deps() with a custom exclude mechanism, or at minimum document this limitation.

Suggested change

# Get dependencies from DESCRIPTION in the current directory

deps <- remotes::dev_package_deps(dependencies = TRUE)

# Filter out rJava to ensure no Java is installed

packages_to_install <- deps$package[deps$package != "rJava"]

# Install/Update the selected packages

if (length(packages_to_install) > 0) {

# We use install_cran to handle versions if specified in DESCRIPTION (though usually remotes::install_deps does this better)

# But since we need to exclude one, we pass the vector.

# remotes::install_cran will install the latest CRAN version.

# To respect version requirements in DESCRIPTION, strictly speaking we should use something more sophisticated,

# but for a dev container, latest versions of dependencies are usually desired.

remotes::install_cran(packages_to_install)

}

# Install dependencies from DESCRIPTION in the current directory

# Use install_deps so that version requirements in DESCRIPTION are respected,

# while excluding rJava to avoid requiring a Java installation in the dev container.

remotes::install_deps(dependencies = TRUE, exclude = "rJava")

Copilot · 2026-01-11T23:29:40Z

.devcontainer/setup.R

+
+# Install/Update the selected packages
+if (length(packages_to_install) > 0) {
+  # We use install_cran to handle versions if specified in DESCRIPTION (though usually remotes::install_deps does this better)


The comment mentions "install_cran" but the actual function call is "remotes::install_cran". The comment should clarify that this is the remotes package function being used, not a hypothetical local function.

Suggested change

# We use install_cran to handle versions if specified in DESCRIPTION (though usually remotes::install_deps does this better)

# We use remotes::install_cran to handle versions if specified in DESCRIPTION (though usually remotes::install_deps does this better)

Copilot · 2026-01-11T23:29:40Z

.devcontainer/setup.sh

+# Add air to PATH for the current script execution if needed (though we add it to remoteEnv in devcontainer.json)
+# The installer typically puts it in ~/.local/bin


The comment states that PATH is added to remoteEnv in devcontainer.json, but the PATH modification in line 10 happens during setup, not at runtime. The remoteEnv setting only affects the container environment after setup completes. Consider clarifying that this export is needed for the Air CLI to be available during the remainder of the setup script execution.

Suggested change

# Add air to PATH for the current script execution if needed (though we add it to remoteEnv in devcontainer.json)

# The installer typically puts it in ~/.local/bin

# Ensure air is on PATH for the remainder of this setup script.

# The installer typically puts it in ~/.local/bin; remoteEnv in devcontainer.json

# will add this directory to PATH for future shells after setup completes.

Copilot · 2026-01-11T23:29:40Z

.devcontainer/setup.sh

+
+# Install Posit Air CLI
+echo "Installing Posit Air CLI..."
+curl -LsSf https://github.com/posit-dev/air/releases/latest/download/air-installer.sh | sh


Using curl ... | sh to install air-installer.sh executes a mutable remote script from GitHub without any pinning or integrity verification. If the GitHub repository, release asset, or network path is compromised, an attacker could execute arbitrary code inside the dev container with the same privileges as the developer, potentially exfiltrating source code or credentials. Prefer downloading a specific pinned version and verifying a checksum or signature, or vendoring a trusted installer script into this repository before executing it.

Add devcontainer configuration for R project

7d1190c

- Use `mcr.microsoft.com/devcontainers/r:latest` as base image. - Exclude `rJava` from dependency installation to keep container Java-free. - Install Posit Air CLI and VS Code extension. - Install Quarto extension.

e-kotov marked this pull request as ready for review January 11, 2026 23:26

Copilot AI review requested due to automatic review settings January 11, 2026 23:26

Copilot started reviewing on behalf of e-kotov January 11, 2026 23:26 View session

Copilot AI reviewed Jan 11, 2026

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	# We use install_cran to handle versions if specified in DESCRIPTION (though usually remotes::install_deps does this better)
	# We use remotes::install_cran to handle versions if specified in DESCRIPTION (though usually remotes::install_deps does this better)

		# Add air to PATH for the current script execution if needed (though we add it to remoteEnv in devcontainer.json)
		# The installer typically puts it in ~/.local/bin

-# Add air to PATH for the current script execution if needed (though we add it to remoteEnv in devcontainer.json)
-# The installer typically puts it in ~/.local/bin
+# Ensure air is on PATH for the remainder of this setup script.
+# The installer typically puts it in ~/.local/bin; remoteEnv in devcontainer.json
+# will add this directory to PATH for future shells after setup completes.

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