NEWS

doppelgangR 1.41.1

SummarizedExperiment Support: Added native, seamless support for SummarizedExperiment inputs (and lists containing them) in the main doppelgangR() function. The objects are automatically coerced to ExpressionSet internally using robust S4 coercion (as(x, "ExpressionSet")), enabling direct compatibility without manual type conversions.

Replaced BiocParallel package usage with the CRAN future and future.apply framework for parallel computing.
Removed BPPARAM parameter from doppelgangR() to align with future package best practices (enabling global backend configuration via future::plan()).
Added a dummy parameter catcher in doppelgangR(...) that throws a helpful deprecation warning if legacy BPPARAM is used.

Cartesian Product Vector Optimization: Added a vector fast path in .outer2df to construct coordinates directly using vector replication (rep), yielding a 46x speedup on 2,000 samples and eliminating massive memory spikes from legacy string splits.
Phenotype Distance Lookups: Precalculated value frequencies once per column in phenoDist(), allowing vectorWeightedDist() to perform $O(1)$ lookups instead of scanning columns dynamically. This reduced complexity from cubic to quadratic and achieved a 2.3x speedup on 500 samples.
Hamming Distance Helper Optimization: Replaced length(na.omit(z)) with sum(!is.na(z)) inside vectorHammingDist() for an 8x speedup per call.

Recycling Warning Fixed: Resolved a vector length mismatch recycling warning in doppelgangR() intermediate pruning when smoking guns are enabled. Replaced the element-wise logical OR on vectors of unequal sizes with a robust, key-based merging and subsetting strategy.
BiocCheck & Code Style Compliance:
- Migrated unsafe sapply() calls to type-safe vapply().
- Replaced manual integer ranges (1:...) with seq_len().
- Removed paste() and paste0() from inside error and warning condition signals.
- Replaced raw cat and print calls in trace logging blocks with message().