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

Søren Højsgaard @orenh @end|ng |rom m@th@@@u@dk
Sat Dec 4 16:54:57 CET 2021

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

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