[Bioc-devel] BiocCheck required import

[Thomas Lin Pedersen]

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 <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
>>>> 
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>>