NEWS

path2path 0.99.4

Declared R.utils in Suggests: data.table::fread() needs it to read the gzipped demo matrix that the vignette and read_input_matrix() examples use. Its absence broke the 0.99.3 vignette build on the Bioconductor build machines (it was present locally, which masked the missing declaration).

Changes responding to the first round of Bioconductor review:

path2path() now defaults to verbose = FALSE; build_null_pool() and calibrate_pvalues() gained a verbose argument (default FALSE) gating the per-permutation progress messages, which were previously unconditional. Messages that signal a change of behavior (GPD fit-adequacy fallback, collection-name aliasing, non-default configuration reuse, names appended beyond a user-supplied plot order) remain.
All imported functions are now declared with importFrom() in NAMESPACE.
Function documentation states the class of every parameter.
The vignette gained a section on how the package integrates with the Bioconductor ecosystem and how it differs from per-contrast enrichment packages; the quick-tour chunks explain each parameter and interpret the printed output; and all code chunks are now evaluated, including the Route B calibration (run at B = 50 on the demo data) and the file-based input example, which reads the demo matrix shipped in inst/extdata/zscore_demo.csv.gz.
README rewritten around the user-facing question the package answers, with a copy-paste quick start that runs on the bundled demo data.
Added the WholeGenome biocView.

Replaced repeated per-ranking fgsea tied-statistics warnings with one summary per stage. The summary reports the number of affected rankings and their median and maximum tie fractions; other warnings remain visible.
Applied the same tie reporting to the pooled implementations and added regression tests across Stage 1 and Stage 2 modes.

Added conversion to and from SummarizedExperiment.
Strengthened input validation, reproducibility, and documentation in preparation for Bioconductor review.
When no adequate GPD tail fit can be obtained, calibrate_pvalues() returns pooled empirical p-values instead of extrapolating from an inadequate fit.

Initial Bioconductor submission candidate, implementing two-stage pathway mapping, two significance routes, overlap masking, plotting, and file input/output.