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

stefano m@ng|o|@@te|@no @end|ng |rom gm@||@com
Wed Mar 10 00:14:54 CET 2021


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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