Branched shiny validate to warning

[veitveit]

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[Copilot]

Pull Request Overview

This pull request modernizes the handling of Shiny validation in the pcaWithVar function to support usage both within and outside Shiny applications. The main improvement allows the function to gracefully handle data validation errors in non-Shiny contexts by issuing warnings and returning NULL, rather than attempting to use Shiny's validate() function which only works within reactive contexts.

Key changes:

• Modified pcaWithVar to conditionally use Shiny validation based on runtime context
• Added proper data documentation tags (@docType data, @usage) for dataset documentation
• Updated package metadata (version bump from 1.11.2 to 1.13.1, RoxygenNote 7.3.2 → 7.3.3)

Reviewed Changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
R/PrepareData.R	Added conditional Shiny runtime detection for validation logic; reformatted indentation throughout multiple functions
R/protein_expression.R	Added @docType data and @usage annotations to dataset documentation
R/artificial_clusters.R	Added @docType data and @usage annotations to dataset documentation
NAMESPACE	Added isRunning import from shiny package to support new conditional logic
DESCRIPTION	Updated package version to 1.13.1 and RoxygenNote to 7.3.3
man/protein_expressions.Rd	Updated documentation usage section to use data() function syntax
man/artificial_clusters.Rd	Updated documentation usage section to use data() function syntax
man/pcaWithVar.Rd	Auto-generated documentation reflecting changes to source roxygen comments
inst/docker/Dockerfile	Commented out RDAVIDWebService installation (dependency removal)
..Rcheck/00check.log	Updated R version and compiler information in check log

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