improve "third party code" section

[vjcitn]

The term "third party code" is somewhat vague. We are seeing submissions that attempt to redistribute
standalone binaries in the package, and I don't know that we have a specific policy on this. I don't like
it, but it seems it will be effective in certain circumstances. I think we should state that the redistribution of
binaries can be allowed with explicit licensing for redistribution included with the package; package must
meet all size requirements with the included binaries, and should be checkable on all three platforms.

Another way to handle a binary is to include code for platform-specific installation of the binary in BiocFileCache?

This is coming up in connection with a prospective submission https://github.com/neurogenomics/MAGMA_Celltyping/blob/bschilder_dev/DESCRIPTION ... which would like to redistribute https://ctg.cncr.nl/software/magma.

[vjcitn]

One question is whether one could think of "Depends/Imports" relationships as use of third-party code. Do we have suggestions on controlling dependencies in this document system? In response to one question about avoiding dependence on minfi to get 450k annotation I proposed

get450kAnno = function() {
  ca = BiocFileCache::BiocFileCache()
  q = BiocFileCache::bfcquery(ca, "450kanno.ilmn12.hg19")
  if (length(q$rpath)>0) return(readRDS(rev(q$rpath)[1])) # if multiple, use last
  if (!requireNamespace("minfi")) stop("install the minfi package to use this function")
  anno = minfi::getAnnotation("IlluminaHumanMethylation450kanno.ilmn12.hg19")
  tf = tempfile()
  saveRDS(anno, tf)
  BiocFileCache::bfcadd(ca, rname="IlluminaHumanMethylation450kanno.ilmn12.hg19", fpath=tf,
    action="move")  # for future
  anno
}

Better to import BiocFileCache than minfi. This might be a basis for a suggestion of somewhat broader scope.