[Bioc-devel] False positive BiocCheck? Packages providing 5 object(s) used in this package should be imported in the NAMESPACE

[stefano]

Thanks Martin,



I have dropped the @ call.



Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544



*From: *Martin Morgan <mtmorgan.bioc using gmail.com>
*Sent: *Wednesday, 10 March 2021 11:36 AM
*To: *stefano <mangiolastefano using gmail.com>; bioc-devel
<bioc-devel using r-project.org>
*Subject: *Re: [Bioc-devel] False positive BiocCheck? Packages providing 5
object(s) used in this package should be imported in the NAMESPACE



It looks like you're assigning to assays, `assays(x) <- ...`, so you need
to import `assays<-`, and not just `assays`.



But this



  assays(new_obj)@listData <-



looks VERY BAD. The internal structure of the assays slot (accessed with @)
should NEVER be accessed directly; use the public 'API' only.



Martin



On 3/9/21, 6:15 PM, "Bioc-devel on behalf of stefano" <
bioc-devel-bounces using r-project.org on behalf of mangiolastefano using gmail.com>
wrote:



    Hello,



    I have a trouble for tidySummarizedExperiment package BiocCheck()



    This is BiocCheck version 1.26.0. BiocCheck is a work in progress.

    Output and severity

    of issues may change. Installing package...* Checking Package

    Dependencies...* Checking if other packages can import this one...

    * ERROR: Packages providing 5 object(s) used in this package should be

    imported in

          the NAMESPACE file, otherwise packages importing this package

    may fail.

          package::object in function()

            SummarizedExperiment::assays<- in
bind_rows.SummarizedExperiment()





    However NAMESPACE includes



    importFrom(SummarizedExperiment,assays)



    And my method is specified as



    #' @importFrom rlang dots_values

    #' @importFrom rlang flatten_if

    #' @importFrom rlang is_spliced

    #' @importFrom SummarizedExperiment cbind

    #' @importFrom SummarizedExperiment assays

    #'

    #' @export

    #'

    bind_rows.SummarizedExperiment <- function(..., .id=NULL,

    add.cell.ids=NULL) {

        tts <- flatten_if(dots_values(...), is_spliced)



        new_obj <- cbind(tts[[1]], tts[[2]])



        # If duplicated cell names

        if (new_obj %>% colnames() %>% duplicated() %>% which() %>% length()

    %>% gt(0)) {

            warning("tidySummarizedExperiment says: you have duplicated
sample

    names, they will be made unique.")

        }

        unique_colnames <- make.unique(colnames(new_obj), sep="_")



        colnames(new_obj) <- unique_colnames



        # Change also all assays colnames

        assays(new_obj)@listData <- assays(new_obj)@listData %>% map(~ {

            colnames(.x) <- unique_colnames

            .x

        })



        new_obj

    }



    Is there something I am missing?



    Best wishes.



    *Stefano *







    Stefano Mangiola | Postdoctoral fellow



    Papenfuss Laboratory



    The Walter Eliza Hall Institute of Medical Research



    +61 (0)466452544



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