Set available_package_filters option before calling pkgAvail() directly/indirectly

[hturner]

miniCRAN::pkgAvail() calls utils::available.packages() with filters = NULL by default. As documented in ?available.packages, this corresponds to a default set of filters: c("R_version", "OS_type", "subarch", "duplicates"), which means that it excludes packages whose OS requirement is incompatible with the current OS and excludes those with compiled code that is not available for the current sub-architecture.

In other words, running offlinedatasci install r-packages tmp on Windows excludes packages that are compiled for macOS, which is quite a lot!

Unfortunately miniCRAN::makeRepo calls pkgAvail() without setting any filters argument, so the only way to control this at the moment is to set the available_packages_filters option. I think you want:

options(available_packages_filters = "duplicates")

Also dropping "R_version" as this is already handled by setting the URL and potentially someone could try setting up a miniCRAN for R 4.4 (say) when their current version of R is a different version.

[ethanwhite]

Thanks for this @hturner! Can you provide a specific example of the differences you see with and without options(available_packages_filters = "duplicates") so that we can compare to that. A few quick examples on Linux didn't show any differences so we're just trying to figure out where to look.

[hturner]

Yes, here's one:

repos <- "https://cloud.r-project.org"
type <- "mac.binary.big-sur-arm64"
pp <- available.packages(miniCRAN:::contribUrl(repos, type, "4.4"), 
                         type = type, 
                         filters = c("R_version", "OS_type",
                                     "subarch", "duplicates"))
pp["fs", 1:3]
#> Error in pp["fs", 1:3]: subscript out of bounds
pp <- available.packages(miniCRAN:::contribUrl(repos, type, "4.4"), 
                         type = type, filters = "duplicates")
pp["fs", 1:3]
#>  Package  Version Priority 
#>     "fs"  "1.6.4"       NA

^{Created on 2024-05-16 with reprex v2.1.0}

Also jsonlite was another. They have Archs: <package_name>.so.dSYM in https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.4/PACKAGES.

[ethanwhite]

Thanks @hturner! Looks like it is pretty likely that the miniCRAN maintainer will have a fix in for this shortly so we're going to let this sit for a week or so and see if we can make a minimal change relying on the upstream fix. If it doesn't come in soon we'll either work around with options() or install straight from the GitHub dev branch.