>From a very quick look at this, I think you also need to explicitly
install the package itself for it to be available in external R
session (contrary to when using forked processing as on Linux and
macOS). Something like this:
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
install.packages(".", repos=NULL, type="source") ## needed by
parallel workers
shell: Rscript {0}
That's what I had to do when testing 'future'
(https://github.com/HenrikBengtsson/future/blob/1835a122764bbc0196c78be6da6973c8063922b3/.github/workflows/R-CMD-check.yaml#L69).
/Henrik
On Wed, Jul 29, 2020 at 10:18 AM Giulia Pais <giuliapa...@gmail.com> wrote:
>
> Hi bioconductor team,
>
> we are currently developing a package for future submission on
> bioconductor which you can find here
> https://github.com/calabrialab/ISAnalytics.
>
> We use Github actions to keep track of R cmd checks at every commit, and
> this time, surprisingly for us, we had a failure on R cmd checks for
> windows (which is odd, since we develop on windows and performing check
> on 2 different windows machines didn't raise any error or warning) and
> we suspect this could be tied to the use of BiocParallel. For Windows,
> in fact, we use SnowParam instead of MulticoreParam and as the vignette
> and manual of BiocParallel specifies we must ensure that every worker is
> loaded with the proper dependencies, but apparently this is not
> necessary if the function to execute in bplapply belongs to the package
> in question. Here is the code of the function that might raise some
> problems:
>
> .import_type <- function(q_type, files, workers) {
> files <- files %>% dplyr::filter(.data$Quantification_type == q_type)
> # Register backend according to platform
> if (.Platform$OS.type == "windows") {
> p <- BiocParallel::SnowParam(workers = workers, stop.on.error = FALSE)
> } else {
> p <- BiocParallel::MulticoreParam(workers = workers, stop.on.error
> = FALSE)
> }
> # Import every file
> suppressMessages(suppressWarnings({
> matrices <- BiocParallel::bptry(
> BiocParallel::bplapply(files$Files_chosen, FUN = function(x) {
> matrix <- ISAnalytics::import_single_Vispa2Matrix(x)
> }, BPPARAM = p)
> )
> }))
> BiocParallel::bpstop(p)
> correct <- BiocParallel::bpok(matrices)
> imported_files <- files %>% dplyr::mutate(Imported = correct)
> matrices <- matrices[correct]
> # Bind rows in single tibble for all files
> if (purrr::is_empty(matrices)) {
> return(NULL)
> }
> matrices <- purrr::reduce(matrices, function(x, y) {
> x %>% dplyr::bind_rows(y) %>% dplyr::distinct()
> })
> list(matrices, imported_files)
> }
>
> The report of the Github action can be found here:
> https://github.com/calabrialab/ISAnalytics/runs/923261561
>
> The check apparently fails with these warnings: Warning - namespace
> 'ISAnalytics' is not available and has been replaced. We tried adding
> 'library(ISAnalytics)' and 'require(ISAnalytics)' but if we do that
> BiocCheck fails with a warning, prompting for removal of this lines.
> Could this be a real issue with our package or just a problem with
> Github actions?
>
> Thanks in advance,
>
> Giulia Pais
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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