(I assume you just forgot to 'Reply All' so I've added bioc-devel back to the cc:)
> Unfortunately what I'm mentioning only happens in Github actions, which > are the standard ones (we used usethis::use_github_action_check_standard), I'd say that that 'usethis' setup did not anticipate package tests that run parallel code. So, don't assume it's perfect and that it covers all use cases. > we haven't modified the action ... That's actually my suggestion - did you try my one-line addition? I'm 95% certain it will solve your check errors on Windows as it did for me. > ... It also appears same actions performed on MacOS have > some kind of problems since they stop even before checking the package. Yes, there seems to be some hiccups. I also get those since a few days back. These are out of our control and we just have to wait for them to resolved upstream/elsewhere. /Henrik On Thu, Jul 30, 2020 at 2:05 AM Giulia Pais <giuliapa...@gmail.com> wrote: > > Thanks for the reply, > > Unfortunately what I'm mentioning only happens in Github actions, which > are the standard ones (we used > usethis::use_github_action_check_standard), we haven't modified the > action, errors I'm mentioning do not happen in local R environments on > windows machines. It also appears same actions performed on MacOS have > some kind of problems since they stop even before checking the package. > > Is it relevant for a bioconductor reviewer the result of these Github > action reports? We would like to submit the package for moderation soon > but we're unsure if we can due to this problem. Thank you. > > Il 29/07/2020 19:25, Henrik Bengtsson ha scritto: > > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel