Gdr 3287

[darsoo]

Description

What changed?

Related JIRA issue: GDR-3287

Why was it changed?

The change was made to ensure compatibility with R 4.5.0 and Bioconductor standards

Logistic checklist

• Package version bumped
• Changelog updated

[gemini-code-assist]

Summary of Changes

Hello @darsoo, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on maintaining the package's health and compatibility within the R and Bioconductor ecosystem. It includes an essential fix for a byte-compilation warning, a minor refactoring of an internal data structure for better code organization, and improvements to the clarity of the package's documentation vignettes.

Highlights

• R 4.5.0 and Bioconductor Compatibility: The package has been updated to ensure compatibility with R 4.5.0 and adhere to Bioconductor standards, specifically addressing stack imbalance warnings during byte-compilation.
• Internal Code Refactoring: The EXCEPTION_TABLE in R/exceptions.R has been refactored by moving its definition inside the get_exception_data function, improving scope management and potentially reducing global namespace pollution.
• Vignette Clarity Improvements: R code chunks within the package vignettes have been systematically renamed to be more descriptive and consistent, enhancing readability and maintainability for documentation.

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Changelog

• DESCRIPTION
  • Updated package version from 1.9.6 to 1.9.7
  • Updated package date from 2026-01-27 to 2026-02-16
• NEWS.md
  • Added a new changelog entry for version 1.9.7
  • Included a note about fixing stack imbalance warnings during byte-compilation
• R/exceptions.R
  • Moved the EXCEPTION_TABLE definition from global scope into the get_exception_data function
• vignettes/ConvertingMAEtoPharmacoSet.Rmd
  • Renamed R code chunks for better clarity (e.g., knitr-options, load-libraries, load-mae-data, inspect-mae-assays, convert-mae-to-pset, display-pset-object, inspect-metadata, inspect-tre-rows, inspect-tre-cols, subset-tre-data-table, invert-subset-tre, view-tre-assays, view-tre-assay-names, inspect-metrics-assay, session-info)
• vignettes/ConvertingPharmacoSetToGDR.Rmd
  • Renamed R code chunks for better clarity (e.g., knitr-init, load-deps, get-pset-example, load-mocked-psets, convert-pset-to-dt, subset-by-cell-line, run-gdr-pipeline, convert-se-to-dt, reset-identifiers, session-info)
• vignettes/gDRimport.Rmd
  • Renamed R code chunks for better clarity (e.g., init-import, load-test-datasets, execute-data-loading, process-prism-level5, process-prism-level6, session-info)

Activity

• The pull request is related to JIRA issue GDR-3287.
• The package version was bumped as part of the changes.
• The changelog was updated to reflect the new version and fixes.
• The changes were made to ensure compatibility with R 4.5.0 and Bioconductor standards.

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[gemini-code-assist]

Code Review

This pull request updates the package version and changelog, and refactors code to address byte-compilation warnings, which is a good improvement. The changes in the R Markdown vignettes to add descriptive labels to code chunks enhance maintainability. I have one suggestion for the R/exceptions.R file to improve performance by avoiding the recreation of a data structure on every function call, using a common R pattern.