[R-pkg-devel] Cascade effect of non-available packages?

[Tiago Olivoto]

Dear all,
Thanks for your prompt reply.

Dear Dirk, check_ebi() was added in the new version at the location I
believe might be triggering the error:

https://github.com/NEPEM-UFSC/pliman/blob/24a1781073f9b1a3141002f0985b0542b1f7178d/R/utils_imagem.R#L317

check_ebi <- function(){
  if(!requireNamespace("EBImage", quietly = TRUE)) {
    if(interactive() == TRUE){
      inst <-
        switch(menu(c("Yes", "No"), title = "Package {EBImage} required but
not installed.\nDo you want to install it now?"),
               "yes", "no")
      if(inst == "yes"){
        if(!requireNamespace("BiocManager", quietly = TRUE)) {
          install.packages("BiocManager", quiet = TRUE)
        }
        BiocManager::install("EBImage",
                             update = FALSE,
                             ask = FALSE,
                             quiet = TRUE)
      } else{
        message("To use {pliman}, first install {EBImage} following the
directions at 'https://bioconductor.org/packages/EBImage'")
      }
    }
  }
}

Looking just now to the function, I realized that it will only work in an
interactive section. I'm not sure if it could be the source of the error
during the checks, because the latest stable version of pliman already
contained it and worked with no erros (but this could be related to the new
version of R or something indirectly related to it).

Anyway, I would appreciate any suggestions to make check_ebi() more robust,
mainly regarding on the way it is handled in the automatic CRAN checks.


Best regards,



Em dom., 3 de nov. de 2024 às 13:10, Georgi Boshnakov <
georgi.boshnakov using manchester.ac.uk> escreveu:

> A lot of packages are erring on CRAN at the moment. From time to time
> weird things happen en masse. It is better to wait a little for
> intermittent problems to clear themselves out, especially during the
> weekend.
>
> Georgi Boshnakov
>
> Sent from Outlook for Android <https://aka.ms/AAb9ysg>
> ------------------------------
> *From:* R-package-devel <r-package-devel-bounces using r-project.org> on behalf
> of Dirk Eddelbuettel <edd using debian.org>
> *Sent:* Sunday, November 3, 2024 2:17:21 PM
> *To:* Tiago Olivoto <tiagoolivoto using gmail.com>
> *Cc:* R Package Devel <r-package-devel using r-project.org>
> *Subject:* Re: [R-pkg-devel] Cascade effect of non-available packages?
>
>
> On 3 November 2024 at 11:02, Tiago Olivoto wrote:
> | Today, I noticed that several stable packages, such as Rcpp and sf, were
> | unavailable during the check process for this submission. This wasn’t an
> | issue in the previously published version of pliman. Could this be a
> | temporary problem with the package availability on CRAN?
>
> I could be. (Auto-)build systems for 21k packages and 3 architectures can
> be
> fragile, and we are in time of transition (R 4.4.2 just came about) so this
> could have been spurious.  If in doubt, check the status of a given package
> at its CRAN page. But I looked at the log links yu provided, and I saw no
> build failure over 'missing Rcpp and/or sf' there.  Can you point us to an
> error?
>
> Moreover, reading
>
> https://urldefense.com/v3/__https://win-builder.r-project.org/incoming_pretest/pliman_3.0.0_20241102_181842/specialChecks/noSuggests/summary.txt__;!!PDiH4ENfjr2_Jw!Af5Xuvyms6hGqaC8rcf5EXqH8icVsEPEbdr4dvBxDrdeNRZb4hlwLZo9QccOefhWkiYMiOT4lFhp93zWR5eCbGaJ$
> [win-builder[.]r-project[.]org]
> I do not see your aforementioned 'check_ebi()' function at work. The
> suggested package is not present, you are asked to not fail and just skip
> but do not seem to do so. I think you need to fix that, and that the CRAN
> messaging is fairly clear and standard here. I may of course have missed
> something in which case 'my bad'.
>
> Dirk
>
> --
> dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org
>
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