[R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

[Tiago Olivoto]

Thanks Duncan,
I'm in the way of a new CRAN submission and I will make sure to call
check_ebi() in the body of each function. This should ensure that the check
for EBImage will be called even with pliman::object_edge( ... ), for
example.

Best regards,
Olivoto

Em qui., 16 de mar. de 2023 às 14:15, Duncan Murdoch <
murdoch.duncan using gmail.com> escreveu:

> On 16/03/2023 12:36 p.m., Tiago Olivoto wrote:
> > Hi,
> > My package pliman depends on EBImage which is in Bioconductor. I have
> > created a function check_ebi() <
> >
> https://github.com/TiagoOlivoto/pliman/blob/e6efc4b6a2396600939e308c235aeb9ab47af375/R/utilities.R#L534
> >
> > that is called in .onAttach() <
> > https://github.com/TiagoOlivoto/pliman/blob/master/R/zzz.R#L36>  and
> checks
> > if EBImage is installed. If not, the function asks the user to install
> it.
>
> If some other package loads but doesn't attach pliman, and is missing
> EBImage, does it fail gracefully?  That's also important.  I'd test what
> happens if a user runs pliman::object_edge( ... ) .  (That function
> isn't in the CRAN version, just the Github version, so I haven't tried
> this.)
>
> Duncan Murdoch
>
>
> > Both EBImage and BiocManager are listed as suggests <
> > https://github.com/TiagoOlivoto/pliman/blob/master/DESCRIPTION#L22>
> >
> > I believe that this could be a possible solution
> > Best regards,
> > Olivoto
> >
> >
> > Em qui., 16 de mar. de 2023 às 11:18, Ruff, Sergej <
> > Sergej.Ruff using tiho-hannover.de> escreveu:
> >
> >> I am currently building a package which uses the "limma"-package as a
> >> dependency.
> >>
> >> I want to submit my package to CRAN.
> >>
> >> Do I need to declare Bioconductor-dependencies such as Limma differently
> >> in the Description-File of my Package?
> >>
> >> The Check-Function in R shows no Notes, Warnings or Errors, but I am not
> >> sure if that means that limma will install when installing my package
> from
> >> CRAN.
> >>
> >> Currently I am declaring limma like this:
> >>
> >> Suggests:
> >>
> >>      limma
> >>
> >>
> >>
> >> Can CRAN identify that limma is a Bioconductor-Package and will it Limma
> >> install, when installing my package from CRAN?
> >>
> >>          [[alternative HTML version deleted]]
> >>
> >> ______________________________________________
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> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>

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