Coding-agent fixes to get RcisTarget passing Bioc build/check/test

[lwaldron]

Hi Stein, I'm part of the Bioconductor leadership (VP of the technical advisory board) and am developing a "rescue" system for Bioconductor packages at https://github.com/bioc-package-rescue. This is the first package I have tested it on, since 1) it's slated for deprecation, and 2) it has a lot of downloads. This PR fixes all ERRORs and some easier WARNINGs; see https://github.com/bioc-package-rescue/RcisTarget/actions/runs/29108369941. Please take a look, and if it looks OK, merge, push upstream to the devel and cherry-pick to RELEASE_3_23, and email Lori Shepherd <lori.shepherd@roswellpark.org > to request de-deprecation. Let me know if you have any questions, whether you do want to keep RcisTarget alive, and whether this is helpful. Thanks, -Levi

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Pull Request: Modernize Package Metadata and Fix iGraph Coercion Issues

Summary

This pull request resolves critical check failures, warnings, and styling issues in RcisTarget to restore compatibility with the latest Bioconductor check pipelines.

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Changes

1. Fix igraph Coercion and Incidence Errors

• Updated Deprecated API: Replaced the deprecated graph.incidence() call with graph_from_incidence_matrix() to restore compatibility with newer versions of the igraph package.
• Added Matrix Coercion: Coerced subsets of data.table and data.frame objects to a numeric matrix via as.matrix() before passing them to the network generation function.
• Robust Column Selection: Dynamically resolved the "rankAtMax" column position index via match() with an safety check to prevent indexing failures.

2. Modernize Package Metadata

• Transitioned to Authors@R: Removed the deprecated Author and Maintainer fields from DESCRIPTION and fully migrated them to the modern Authors@R structure with proper role designations (e.g., [cre]).

3. Guard Suggested Database Example Dependencies

• Added requireNamespace Checks: Guarded examples that depend on the suggested rankings database RcisTarget.hg19.motifDBs.cisbpOnly.500bp with if (requireNamespace(..., quietly = TRUE)) blocks. This avoids hard errors in testing and user environments where suggested datasets might not be pre-installed.

4. Code Style & Quality Cleanup

• Logical Shorthand Conversion: Replaced deprecated logical shorthand usage (e.g. T and F, with=F) with explicit TRUE and FALSE values across multiple R source files to satisfy BiocCheck style guidelines.

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Verification

• Checked packages locally on bioconductor/bioconductor_docker:devel container image.
• Verified that the package successfully completes R CMD check and BiocCheck with zero errors.

[Copilot]

Pull request overview

This PR updates RcisTarget to pass current Bioconductor build/check by modernizing package metadata, tightening R style compliance, and making documentation/examples more robust against missing suggested resources.

Changes:

• Modernizes DESCRIPTION by migrating Author/Maintainer to Authors@R.
• Updates examples/docs to avoid hard failures when the suggested rankings DB package is not installed, and updates deprecated igraph example usage.
• Replaces shorthand logical constants / data.table arguments (T/F, with=F) with explicit TRUE/FALSE, plus adds a Bioconductor check GitHub Actions workflow.

Reviewed changes

Copilot reviewed 9 out of 13 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
R/priv_calcErn.R	Replaces na.rm=T with na.rm=TRUE in ranking matrix initialization.
R/aux_getDbRegionsLoc.R	Replaces \dontrun{} example with a runnable arrow/feather-based example.
R/aux_convertToTargetRegions.R	Replaces \dontrun{} example with a runnable GRanges example.
R/aux_addLogo.R	Replaces invert = T and with=F with TRUE/FALSE.
R/02_addMotifAnnotation.R	Replaces with=F with with=FALSE in a data.table subset.
man/getDbRegionsLoc.Rd	Mirrors the new runnable arrow/feather example in Rd.
man/convertToTargetRegions.Rd	Mirrors the new runnable GRanges example in Rd.
man/calcAUC.Rd	Guards workflow example behind requireNamespace() for suggested rankings DB package.
man/addSignificantGenes.Rd	Updates incidence-matrix example column selection and replaces deprecated igraph example call.
inst/examples/example_workflow.R	Guards workflow script behind requireNamespace() for suggested rankings DB package.
inst/examples/example_addSignificantGenes.R	Updates igraph incidence plotting example.
DESCRIPTION	Migrates to Authors@R.
.github/workflows/check-bioc.yml	Adds Bioconductor-flavored R CMD check workflow via reusable workflow.

Files not reviewed (4)

• man/addSignificantGenes.Rd: Generated file
• man/calcAUC.Rd: Generated file
• man/convertToTargetRegions.Rd: Generated file
• man/getDbRegionsLoc.Rd: Generated file

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