[Bioc-devel] BiocCheck required import

[Dan Tenenbaum]

----- Original Message -----
> From: "Thomas Dybdal Pedersen" <thomasp85 at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: bioc-devel at r-project.org
> Sent: Thursday, September 3, 2015 8:25:36 AM
> Subject: Re: [Bioc-devel] BiocCheck required import
> 
> Sure, sorry. Its available on GitHub at thomasp85/FindMyFriends
> 


Thanks. OK, this is a bug in BiocCheck. It's not immediately clear to me what the best way is to fix it.
So in the meantime you can just ignore this part of the output of BiocCheck. 

Thanks,
Dan


> > 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
> >>>    [[alternative HTML version deleted]]
> >>> 
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> 
> >> _______________________________________________
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> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> 
>