NEWS

EMTscore 0.99.10

Reworded the correlate_sample_scores() error handler message ("Invalid correlation for ..." instead of "Error in correlation for ...") so it no longer triggers the BiocCheck note about redundant 'stop' and 'warn*' wording in signal conditions.
Used <- instead of = for the two remaining top-level assignments in the vignette (colors and emt_names), clearing the lintr assignment_linter output.

Version bump to re-trigger the build after a transient missing-dependency error (GSVA / ScaledMatrix / BiocSingular) on the Bioconductor build system; no package code changes.

Subset the bundled filtered.c2.gmt gene-set file to 500 representative pathways so the vignette (and R CMD check) completes well within the 10-minute time limit; the pathway-correlation example is unchanged in spirit.

Removed the non-standard 'BiocType' DESCRIPTION field that triggered an "Unknown or non-standard DESCRIPTION field(s)" warning in R CMD check; the package is already declared as Software via biocViews.

Further Bioconductor review responses:
Replaced the remaining import() directives with selective importFrom(), keeping import() only where whole-package access is required (ggplot2, and mclust / Matrix for S4 method dispatch).
Replaced direct Seurat @meta.data slot access with accessors ([[ ]], AddMetaData) in the single-cell scoring functions.
Vignette now saves and restores the user's options() and adds a comparison to related Bioconductor gene-set scoring packages in the Introduction.
Added inst/script/make-data.R documenting the provenance and creation of every data/ object, referenced from each data man page.
Fixed the orientation of Execute_SCSE_parallel() so its output matches the other parallel scorers (samples x gene sets).

Responded to the Bioconductor package review:
Rewrote Title and Description without single quotes and wrapped them.
Wrapped Authors@R and added the maintainer ORCID and funder (fnd) entries.
Added 'BiocType: Software' and replaced the data-experiment biocViews with Software biocViews.
Switched parallel execution to BiocParallel and file downloads to BiocFileCache.
Read GMT gene sets with GSEABase and removed the redundant custom reader.
Vectorised correlate_sample_scores() and removed blanket tryCatch() calls and utils::globalVariables().
Reworked the vignette to use BiocStyle, a generated table of contents and an installation section, and to demonstrate SummarizedExperiment / SingleCellExperiment input.
Expanded the unit test suite and moved Figure1.png to man/figures.

Development iterations before the Bioconductor review: refined function documentation and examples, corrected gene set file names, and updated the vignette.