You would do better posting this on r-package-devel rather than here, I
believe.
Bert Gunter
"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
On Sun, Oct 11, 2020 at 11:51 AM Søren Højsgaard <sor...@math.aau.dk> wrote:
> Dear all,
>
> My gRbase package imports functionality from the bioconductor packages
> graph, Rgraphviz and RBGL.
>
> To make installation of gRbase easy, I would like to have these
> bioconductor packages installed in connection with installation of gRbase,
> but to do so the user must use setRepositories() to make sure that R also
> installs packages from bioconductor.
>
> Having to call setRepositories causes what can perhaps be called an
> (unnecessary?) obstacle. Therefore I have been experimenting with deferring
> installation of these bioc-packages until gRbase is loaded the first time
> using .onAttach; please see my attempt below.
>
> However, if the bioc-packages are not installed I can not install gRbase
> so that does not seem to be a viable approach. (The bioc-packages appear as
> Imports: in DESCRIPTION).
>
> Can anyone tell if it is a futile approach and / or perhaps suggest a
> solution. (I would guess that there are many CRAN packages that use
> bioc-packages, so other people must have faced this challenge before).
>
> Thanks in advance.
>
> Best regards
> Søren
>
>
>
>
>
> .onAttach<-function(libname, pkgname) {
>
> ## package startup check
> toinstall=c(
> "graph",
> "Rgraphviz",
> "RBGL"
> )
>
> already_installed <- sapply(toinstall, function(pkg)
> requireNamespace(pkg, quietly=TRUE))
>
> if (any(!already_installed)){
> packageStartupMessage("Need to install the following package(s): ",
> toString(toinstall[!already_installed]),
> "\n")
> }
>
> ## install if needed
> if(!base::all(already_installed)){
> if (!requireNamespace("BiocManager", quietly=TRUE))
> install.packages("BiocManager")
> BiocManager::install(toinstall[!already_installed],
> dependencies=TRUE)
> }
> }
>
>
>
> [[alternative HTML version deleted]]
>
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>
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