NEWS

bgns 0.4.3 (2026-09-27)

Restore Windows builds by removing an unnecessary platform-specific R header.
Emit each tidy self-correlation edge once across processing panels.
Bound neighbor counts by available candidates and prevent integer overflow in top-k buffers.
Preserve independent dimension names for rectangular correlation matrices.
Require unique, non-missing column names for named edge outputs.
Use bounded weighted deviations to improve numerical stability under extreme rescaling while preserving the documented estimator.
Initialize optional SIMD dispatch safely when panel workers start concurrently.
Validate the estimator against an independent R reference and remove the incompatible WGCNA equality assertion and unused suggested dependency.
Expand regression coverage and align sparse help examples and runtime-control documentation.

Prepared the source tree for CRAN review: corrected package metadata and the source-level CITATION evaluation.
Updated sparse Matrix coercion to avoid the deprecated direct triplet-to-dgCMatrix route.
Undefined self-correlations for constant, all-missing, or ineligible columns now remain NA rather than being forced to 1.
Positive-integer arguments now reject non-integral values instead of silently truncating them.
Applied min_overlap consistently to fully finite dense fast paths as well as NA-aware paths.
Fixed the NA-aware sparse self-KNN path, including overlap-specific denominators and stored non-finite values.
Added internal engine helpers for controlled parallel loops, thread limits, runtime SIMD detection, blocked panel traversal, tiny top-k maintenance, sparse dgCMatrix summaries, and safe interrupt checks.
Renamed the mixed dense/sparse native KNN entry point to C_bicor_knn_spdem.
Kept the public API focused on bicor() and bicor_knn() while strengthening the native execution layer.
Preserved exact bicor and exact KNN semantics while improving maintainability and long-running job interruptibility.

Fixed dense bicor(x, y) matrix indexing for rectangular x/y inputs.
Added native mixed dense/dgCMatrix support for bicor_knn(x, y).
Made dense bipartite KNN factor-level handling match the sparse path.
Linked BLAS portably through $(BLAS_LIBS) $(FLIBS) on Unix-like and Windows builds.
Updated the optional WGCNA parity test to use pairwise-complete observations and a single WGCNA thread.

Prepared package metadata, documentation, tests, and vignette for repository review.
Added runnable examples for exported functions.
Clarified signed-threshold semantics in bicor_knn().
Clarified KNN edge direction and bipartite behavior.
Honored pairwise.complete.obs in the native KNN interface.
Removed generated vignette artifacts from the source tree.
Removed hard-coded local macOS SDK paths from build flags.
Set an explicit C++ standard and capped default OpenMP usage to at most two threads.