[R-pkg-devel] Checking package dependencies before loading namespace
Tiago Olivoto
t|@goo||voto @end|ng |rom gm@||@com
Mon Sep 6 12:43:03 CEST 2021
Thanks to all for the suggestions!
Best,
Tiago
Em sáb., 4 de set. de 2021 às 23:45, Martin Morgan <mtmorgan.bioc using gmail.com>
escreveu:
> 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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>
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