Feature Request: Support system requirements for Bioconductor

[lz100]

Can we add support for Bioconductor packages in pak::pkg_system_requirements function?

I have made a post aslo here.

I know the biggest issue here may be waiting for system requirements of Bioc to be supported on Package Manager.

[jimhester]

There isn't really anything that needs to be done for pak here. Bioconductor system requirements are already supported by the RStudio Package Manager, the Bioconductor specific system requirements would just need to be added to the catalog by the Bioconductor community.

[michaelmayer2]

There isn't really anything that needs to be done for pak here. Bioconductor system requirements are already supported by the RStudio Package Manager, the Bioconductor specific system requirements would just need to be added to the catalog by the Bioconductor community.

Just stumbling across this ticket while exploring pak.

It looks like Bioconductor lists SystemRequirements for their packages.

For pakthe current approach is to by default resolve system requirements for CRAN packages only. If Bioconductor is needed, one could define

Sys.setenv(RSPM_REPO_ID=1)
system(pkg_system_requirements(cran_packages, "ubuntu", "22.04"))
Sys.setenv(RSPM_REPO_ID=4)
system(pkg_system_requirements(bioconductor_packages, "ubuntu", "22.04"))

to install system requirements for both cran_packages and bioconductor_packages (both variables can be a string or a list with r packages). Sadly so this does not work for Bioconductor today because the RSPM API expects bioc_version as part of the RSPM API call

It may be worthwhile to further extend this feature so that multiple RSPM_REPO_IDs including Bioconductor can be checked in one pkg_system_requirements call.