[R] Handling dependencies on Bioconductor packages for packages on CRAN

Bert Gunter bgunter@4567 @end|ng |rom gm@||@com
Sat Dec 4 16:59:27 CET 2021

I suggest you post this on r-package-devel.  That seems a better fit.

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 Sat, Dec 4, 2021 at 7:55 AM Søren Højsgaard <sorenh using math.aau.dk> wrote:

> Dear all
> My gRbase package imports the packages from Bioconductor: graph, RBGL and
> Rgraphviz
> If these packages are not installed, then gRbase can not be installed. The
> error message is:
>    ERROR: dependency ‘graph’ is not available for package ‘gRbase’
> If I, prior to installation, run setRepositories and highlight 'BioC
> software', then gRbase installs as it should, because the graph package
> from Bioconductor is installed along with it. However, this extra step is
> an obstacle to many users of the package which means that either people do
> not use the package or people ask questions about this issue on stack
> overflow, R-help, by email to me etc. It is not a problem to get the
> package on CRAN because, I guess, the CRAN check machines already have the
> three bioconductor packages installed.
> Therefore, I wonder if there is a way of specifying, in the DESCRIPTION
> file or elsewhere, that these packages should be installed automatically
> from bioconductor.
> An alternative would be if one could force the error message
>    ERROR: dependency ‘graph’ is not available for package ‘gRbase’
> to be accompanied by a message about what the user then should do.
> Any good suggestions? Thanks in advance.
> Best regards
> Søren
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