intermingle.cbind: input validation, row-name alignment, safe subsetting, loop fix, docs

[vertesy]

Motivation

• Harden intermingle.cbind() so inputs are validated, rows are matched by name (not position), and column iteration/subsetting is safe to avoid accidental dimension drops.

Description

• Add a compact stopifnot() that asserts (is.data.frame(df1) || is.matrix(df1)), (is.data.frame(df2) || is.matrix(df2)), non-null rownames(df1) and rownames(df2), and ncol(df1) == ncol(df2).
• When row counts differ, subset both df1 and df2 to the intersect(rownames(df2), rownames(df1)) using drop = FALSE to preserve dimensions.
• When row counts match, explicitly reorder df2 to rownames(df1) with df2 <- df2[CommonGenes, , drop = FALSE] so rows are combined by name, not by position.
• Replace for (x in 1:(2 * length(df1))) with for (x in seq_len(2L * ncol(df1))), update the roxygen @return to state a matrix is returned, regenerate man/intermingle.cbind.Rd, and bump Development/config.R version to 2.8.1.

Testing

• Ran git diff --check which reported no issues and used git diff --stat to inspect changes; commit created successfully.
• Attempted Rscript -e 'roxygen2::roxygenise(load_code = roxygen2::load_source)' but Rscript is not available in the environment so automated doc generation failed.
• Man page man/intermingle.cbind.Rd was updated manually to match the new @return text and committed.
• Verified working tree with git status --short and inspected the diffs before committing.

---

Codex Task

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 0c79fe148e

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[vertesy]

@copilot

Could you please address and validate the following issue? And if you agree with it, please fix it.

"Problem: intermingle.cbind() treats equal row counts as proof that every df1 row name exists in df2, so the result can contain missing df2 values or fail during matrix subsetting instead of returning matched rows. Trigger: df1 and df2 have the same number of rows but different row-name sets. Fix: use the intersection path whenever the row-name sets differ, or reject unequal sets before reordering."

[Copilot]

@copilot

Could you please address and validate the following issue? And if you agree with it, please fix it.
...

Addressed in a2054f1. I agreed with the issue and changed intermingle.cbind() to use the intersection/subset path whenever row-name sets differ, even if row counts are equal. Validation: git diff --check passed; secret scan passed; automated code review found no comments; CodeQL had no analyzable code for this R-only change.