[Bioc-devel] ddply causes error during R check

[web working]

Hi Mike,

thank you for pointing out that there are other package which have the 
same situation.

Tobias

Am 12.02.19 um 14:47 schrieb Mike Smith:
> If you're sure these are false positives (and it looks like they are) 
> then you can use utils::globalVariables() outside of your function to 
> get rid of the note.  It might also be worth pointing out that there 
> are also plenty of Bioconductor packages that don't do this and simply 
> have this mentioned in the check results e.g 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/beadarray/malbec2-checksrc.html 
> .
>
> Mike
>
> On Tue, 12 Feb 2019 at 08:35, web working <webworking using posteo.de 
> <mailto:webworking using posteo.de>> wrote:
>
>     Hi,
>
>     I am developing a Bioconductor package and can not get rid of some
>     warning messages. During devtools::check() I get the following
>     warning
>     messages:
>
>     ...
>     summarizeDataFrame: no visible binding for global variable ‘name’
>     summarizeDataFrame: no visible binding for global variable ‘gene’
>     summarizeDataFrame: no visible binding for global variable ‘value’
>     ...
>
>     Here a short version of the function:
>
>     #' Collapse rows with duplicated name column
>     #'
>     #' @param dat a \cite{tibble} with the columns name, gene and value
>     #' @importFrom plyr ddply
>     #' @import tibble
>     #' @return a \cite{tibble}
>     #' @export
>     #'
>     #' @examples
>     #' dat <- tibble(name = c(paste0("position", 1:5), paste0("position",
>     c(1:3))), gene = paste0("gene", 1:8), value = 1:8)
>     #' summarizeDataFrame(dat)
>     summarizeDataFrame <- function(dat){
>        ddply(dat, "name", "summarize",
>              name=unique(name),
>              gene=paste(unique(gene), collapse = ","),
>              value=mean(value))
>     }
>
>     R interprets the "name", "gene" and "value" column names as variables
>     during the check. Does anyone has an idea how to change the syntax of
>     ddply or how to get rid of the warning message?
>
>     Thanks in advance!
>
>     Tobias
>
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