[Bioc-devel] Problems with BiocParallel on Windows

Giulia Pais g|u||@p@|@1 @end|ng |rom gm@||@com
Mon Oct 25 13:00:12 CEST 2021

I tried that also on other functions but it seems also exported functions are invisible to SnowParam workers. That is really odd since it worked just fine before. For now since we're approaching the deadline for the new Bioc release we may opt to switch everything to MulticoreParam despite being just a serial param on Windows. We'll try to figure out what causes this after the new release, thanks

On 10/25/21, 12:57, "Jiefei Wang" <szwjf08 using gmail.com> wrote:

    Hi Giulia,

    One of your errors is raised from L1288 in the file "analysis-functions.R"

    if (getOption("ISAnalytics.verbose") == TRUE) { ... }

    The error message is "argument is of length zero". Usually, this means
    something is wrong with the global option. Then I see at L4812 in
    "internal-functions.R", you have

    p <- BiocParallel::SnowParam(
                    tasks = length(common_names),
                    progressbar = getOption("ISAnalytics.verbose"),
                    exportglobals = FALSE

    Please keep in mind that if you use SnowParam, the worker is a fresh R
    process and independent with your master. Since you have
    `exportglobals = FALSE`, the worker has no idea about the option
    "ISAnalytics.verbose" in your master process and hence the error.

    To fix that, you can set  `exportglobals = TRUE` to let the worker
    know the option. If you do not want to export the globals, you can
    also add the global option "ISAnalytics.verbose" manually at the
    beginning of the function in bplapply.


    On Mon, Oct 25, 2021 at 5:42 PM Giulia Pais <giuliapais1 using gmail.com> wrote:
    > Hello,
    > I’m the developer of the package ISAnalytics. Since the last build we’re having issues with BiocParallel on the Windows platform only. In particular, trying to debug what the issue might be on a local Windows machine, it seems BiocParallel isn’t able to find internal package functions and fails at several jobs that did just fine a few versions ago.
    > We’re using MulticoreParam for Linux and Mac and SnowParam for Windows as suggested, I’m not really sure how to fix this issue and I’ll appreciate any help,
    > Thank you
    > Giulia Pais
    >         [[alternative HTML version deleted]]
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