Fixing R CMD CHECK and re-adding biocparallel

[amcim]

This PR has the purpose of getting R CMD CHECK working again and re-adding essential Bioconductor requirements (BiocParallel).

The main problem with R CMD CHECK was malformed roxygen blocks, mostly in generate_matrices_ml.R. devtools::document() was erroring out partway through, so the .Rd files never regenerated, and that stale documentation is what produced most of the issues. Fixing the roxygen resolved those as a side effect. Additionally some parameters for functions across the package were out of date and were updated.

BiocParallel had been swapped out for future/future.apply. Restored SnowParam(RNGseed = seed) + bplapply(), matching #23.

[eboyer221]

Tested and confirmed that this restores BiocParallel::SnowParam()/bplapply() in runMDRmodels()/runMLmodels() (matching #23) and fixes the malformed roxygen blocks that were breaking devtools::document(). No issues in the lines this PR touches.

[eboyer221]

Confirmed this does what it says: restores BiocParallel::SnowParam()/bplapply() in runMDRmodels()/runMLmodels() (matching #23) and fixes the malformed roxygen blocks that were breaking devtools::document(). Diff is clean and narrowly scoped — no issues in the lines this PR actually touches.

(Found some pre-existing bugs elsewhere in the codebase while reviewing — unrelated to this PR, will file separately.)