[Bioc-devel] set.seed()

[Luigi Cerulo]

We are preparing a new package submission. BiocCheck reports set.seed() at two sites. One is in a verbatim port of the frozen manuscript inference implementation, retained and regression-tested for exact method reproducibility. The other is in an exported simulation function with an explicit user-provided seed= argument; the caller RNG state is restored, and seed=NULL leaves RNG control to the caller. R CMD check is clean and all other BiocCheck warnings have been resolved. Would a documented justification for these two uses be acceptable for submission, or would you require their removal despite the reproducibility/API implications?
Luce