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"
<r-package-devel-boun...@r-project.org on behalf of tiagooliv...@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 <
lig...@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]]
> >>
> >> ______________________________________________
> >> R-package-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
> > ______________________________________________
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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