[R-pkg-devel] Checking package dependencies before loading namespace

[Martin Morgan]

Actually, I think the right thing to do is to tell the user what to do ("To use this feature, install EBImage following the directions at https://bioconductor.org/packages/EBImage') instead of doing it for them.

Martin

From: Tiago Olivoto <tiagoolivoto using gmail.com>
Date: Friday, September 3, 2021 at 2:14 PM
To: Martin Morgan <mtmorgan.bioc using gmail.com>
Cc: Uwe Ligges <ligges using statistik.tu-dortmund.de>, R Package Devel <r-package-devel using r-project.org>
Subject: Re: [R-pkg-devel] Checking package dependencies before loading namespace
Thanks for your response Martin,
I'm definitely thinking to use BiocManager::install("EBImage") since it is the official suggestion of the Bioconductor community. Anyway, I've been learning a lot from this discussion. Thanks all!!
Best,
Tiago

Em sex., 3 de set. de 2021 às 12:58, Martin Morgan <mailto:mtmorgan.bioc using gmail.com> escreveu:
The specific repository you've chosen is not what you want to do. This will always install EBImage from Bioconductor version 3.13, but Bioconductor version 3.13 is only relevant for R-4.1 (see https://bioconductor.org/about/release-announcements/)

Personally, I would encourage you to follow the Bioconductor community best practice of BiocManager::install("EBImage"). In that way you will get the version of EBImage that has been tested with other Bioconductor packages in the same release, and on the version of R in use by your user.

If you were to use a specific repository, it should the one that is as good as base R can do (this can be different from the version that BiocManager would choose because R's release cycle is different from Bioconductor's). I think this is most easily accomplished by utils::chooseBioCmirror(), and then selecting the 0-Bioconductor repository. That's a lot to tell your users... Maybe others in the R community have a better way (the key information is in tools:::.BioC_version_associated_with_R_version(), but that is not an exported function so not recommended for CRAN packages...)

Martin Morgan

On 9/1/21, 8:13 AM, "R-package-devel on behalf of Tiago Olivoto" <mailto:r-package-devel-bounces using r-project.org on behalf of mailto:tiagoolivoto using gmail.com> wrote:

    Thank you, Duncan and Uwe for the suggestions.
     I followed your instructions and created a function to check for EBImage
    that is only called in an interactive section and, if necessary, ask the
    user to install the package with install.packages("EBImage", repos="
    https://bioconductor.org/packages/3.13/bioc")

    Best,
    Tiago

    Em qua., 1 de set. de 2021 às 03:53, Uwe Ligges <
    mailto:ligges using statistik.tu-dortmund.de> escreveu:

    > Two more comments.
    >
    > 1. Note that your code only works in interactice mode, not when checking
    > your package as it waits infinitely for the user's choice.
    >
    > 2. I do not see an advantage of installing BiocManager if EBImage is
    > needed, the essential part is simply to select BioC as a repository to
    > install packages from.
    >
    > Best,
    > Uwe Ligges
    >
    >
    > On 31.08.2021 23:33, Duncan Murdoch wrote:
    > > People shouldn't be able to install your package unless the "hard"
    > > dependencies are available.
    > >
    > > If EBImage isn't essential to your package, you should make it a "soft"
    > > dependency by listing it in Suggests and checking for it every time you
    > > use it.
    > >
    > > Duncan Murdoch
    > >
    > > On 31/08/2021 3:20 p.m., Tiago Olivoto wrote:
    > >> Dear all,
    > >> I have a package called pliman
    > >> <https://CRAN.R-project.org/package=pliman>
    > >> which depends on the Bioconductor package EBImage.
    > >>
    > >> When running install.packages("pliman") I get the following warning
    > >>
    > >> Warning in install.packages :  dependency ‘EBImage’ is not available
    > >>
    > >> and thus when loading the package with library(pliman), the following
    > >> error
    > >> occurs
    > >>
    > >> Erro: package or namespace load failed for ‘pliman’ in loadNamespace(i,
    > >> c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
    > >>   there is no package called ‘EBImage’
    > >>
    > >> I created a check function to check if EBImage is available and if
    > >> not, ask
    > >> users if they want to install it
    > >>
    > >> ---
    > >> check_ebi <- function(){
    > >>    if(!requireNamespace("EBImage", quietly = TRUE)) {
    > >>      inst <-
    > >>      switch(menu(c("Yes", "No"), title = "Package {EBImage} required
    > >> but not
    > >> available.\nDo you want to install it now?"),
    > >>             "yes", "no")
    > >>      if(inst == "yes"){
    > >>        if (!requireNamespace("BiocManager", quietly = TRUE)){
    > >>          install.packages("BiocManager")
    > >>        }
    > >>        BiocManager::install("EBImage", ask = FALSE, update = FALSE)
    > >>      } else{
    > >>        message("To use {pliman}, first install {EBImage} with
    > >> 'BiocManager::install(\"EBImage\")'.")
    > >>      }
    > >>    }
    > >> }
    > >> ---
    > >>
    > >> Is there any way to run this function prior to namespace loading? I
    > tried
    > >> putting check_ebi() into .onLoad() but the same error occurs.
    > >>
    > >> Thanks in advance for any suggestions.
    > >> Tiago
    > >>
    > >>     [[alternative HTML version deleted]]
    > >>
    > >> ______________________________________________
    > >> mailto:R-package-devel using r-project.org mailing list
    > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
    > >>
    > >
    > > ______________________________________________
    > > mailto:R-package-devel using r-project.org mailing list
    > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
    >

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