[Bioc-devel] BiocCheck required import

Thomas Lin Pedersen thomasp85 at gmail.com
Thu Sep 3 10:03:42 CEST 2015

I’m polishing up a package for release and gets this “REQUIRED” message from BiocCheck that kinds of baffles me:

    * REQUIRED: Packages (IRanges, Biostrings) which provide reverse,
      reverse (used in trailsToGraph, trailsToGraph) should be imported
      in the NAMESPACE file, otherwise packages that import
      FindMyFriends could fail.

This is the source code for trailsToGraph:

trailsToGraph <- function(trails) {
    trails <- unlist(lapply(trails, function(x) c(x, NA)))
    edges <- data.frame(from = trails[-length(trails)], to = trails[-1])
    edges <- edges[!is.na(edges$from) & !is.na(edges$to),]
    edges <- edges %>%
        group_by(from, to) %>%
        summarise(weight = length(from))

I do not use reverse() anywhere in my code. Is this a bug in BiocCheck or are there some requirements for imports with packages that shares symbols, even though these symbols are not used?


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