My package will use BiocParallel for permutation test. To make permutations reproducible, I read some discussions online (https://stat.ethz.ch/pipermail/bioc-devel/2015-June/007583.html, https://stackoverflow.com/questions/30610375/how-to-run-permutations-using-mclapply-in-a-reproducible-way-regardless-of-numbe). There are two easy solutions:
(1) Generate the permuted sample indexes before parallel computations. In this way, set.seed() can be used outside of my R function.
(2) Generate a vector of seeds (provided by users through argument of my R function) and use them by set.seed() in each parallel computation.
My permutation scheme is a little complex, so storing sample indexes needs a huge storage space. I have to use the second solution. However, set.seed() will cause warning in BiocCheck(). Could anybody give me suggestions?
Thanks a lot for your help!