[Bioc-devel] BiocCheck required import

From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
To: "Thomas Lin Pedersen" <thomasp85 at gmail.com>
Cc: bioc-devel at r-project.org
Sent: Thursday, September 3, 2015 7:55:42 AM
Subject: Re: [Bioc-devel] BiocCheck required import

What's the name of the package?

Dan


----- Original Message -----

From: "Thomas Lin Pedersen" <thomasp85 at gmail.com>
To: bioc-devel at r-project.org
Sent: Thursday, September 3, 2015 1:03:42 AM
Subject: [Bioc-devel] BiocCheck required import

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))
    graph_from_data_frame(edges)
}

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?

best

Thomas
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