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

Martin Morgan mtmorg@n@b|oc @end|ng |rom gm@||@com
Wed Mar 10 01:36:54 CET 2021

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.


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:


    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


    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


    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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