[Bioc-devel] BiocCheck required import

Den 03/09/2015 kl. 16.57 skrev Dan Tenenbaum <dtenenba at fredhutch.org>:



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

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?

I mean, is the source available somewhere?
Dan

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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