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
best
Thomas
> On 03 Sep 2015, at 19:43, Dan Tenenbaum <dtene...@fredhutch.org> wrote:
>
>
>
> ----- Original Message -----
>> From: "Thomas Dybdal Pedersen" <thomas...@gmail.com>
>> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>> Cc: bioc-devel@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
>>> <dtene...@fredhutch.org>:
>>>
>>>
>>>
>>> ----- Original Message -----
>>>> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
>>>> To: "Thomas Lin Pedersen" <thomas...@gmail.com>
>>>> Cc: bioc-devel@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" <thomas...@gmail.com>
>>>>> To: bioc-devel@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@r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>> _______________________________________________
>>>> Bioc-devel@r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>
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