[Bioc-devel] BiocCheck required import

[Dan Tenenbaum]

----- Original Message -----
> From: "Thomas Lin Pedersen" <thomasp85 at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: bioc-devel at r-project.org
> Sent: Thursday, September 3, 2015 10:50:19 AM
> Subject: Re: [Bioc-devel] BiocCheck required import
> 
> It might be related to the use of globalVariables() to silence R CMD
> CHECK warnings about undeclared symbols when using non-standard
> evaluation in ggplot, dplyr and the likes…
> 
> See the aaa.R file
> 

Yes, I am aware of that. You have a global variable called 'desc' which is also the name of an exported object in IRanges and dplyr. The BiocCheck code assumes that you are trying to use those functions but you are not. I know what I need to do but I'm not sure how to do it in a way that does not limit useful functionality. I will fix it as soon as I figure it out.

Thanks,
Dan


> best
> Thomas
> 
> 
> > On 03 Sep 2015, at 19:43, Dan Tenenbaum <dtenenba at fredhutch.org>
> > wrote:
> > 
> > 
> > 
> > ----- 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
> >>>> 
> >>>> _______________________________________________
> >>>> Bioc-devel at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>> 
> >> 
> 
>