[Bioc-devel] ddply causes error during R check

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 at posteo.de 
<mailto:webworking at 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