More flexible dependency versions filters

[jeroen]

Currently we simply call install.packages() to get dependencies, which always prefers the highest version of each R package. However in some cases may need something else.

For example, in we want 'basilisk.utils' from the first repo, however the one in the second repo is higher.

# Problem: we want 'basilisk.utils' from myrepo even though it has a lower version
db <- available.packages(repos = c(
  myrepo = 'https://bioconductor-source.r-universe.dev',
  bioc = 'https://bioc.r-universe.dev'
))

# Gives us the latter
subset(db, row.names(db) == 'basilisk.utils')

The "filters" argument in availabe.packages() allows us to customize this (search base R source for available_packages_filters_db). For example this should filter duplicates left-to-right I think:

db <- available.packages(repos = c(
  myrepo = 'https://bioconductor-source.r-universe.dev',
  bioc = 'https://bioc.r-universe.dev/'
), filters = list(
  "R_version", 
  "OS_type",
  "subarch",
  function(db){
    db[!duplicated(row.names(db)),]
  }
))

Or to make this apply only to bioc we could do like

options(available_packages_filters = list(
  "R_version", "OS_type", "subarch",
  function(db){
    isbioc <- grepl("https://bioc.r-universe.dev", fixed = TRUE, db[,'Repository'])
    biocdups <- duplicated(row.names(db)) & isbioc
    db[!biocdups,]
  },
  "duplicates"
))

[vjcitn]

Hi -- can you comment on whether this event is a symptom of the same problem? @csoneson pointed this out.

The same error crops up here @hpages

Perhaps this would not be happening if Gviz were explicitly part of the test universe? @LiNk-NY

[hpages]

I see package 'GenomicRanges' 1.60.0 is loaded, but >= 1.61.1 is required by 'Gviz' in the events reported by @vjcitn. This suggests that the runner has a mix of release and devel packages: GenomicRanges 1.60.0 is from BioC 3.21 and the version of Gviz that requires GenomicRanges >= 1.61.1 is from BioC 3.22.

Release and devel packages should never be mixed. This can be avoided by installing Bioconductor deps from the following repositories:

• BiocManager::repositories(version="3.21") when building/checking a BioC 3.21 package (release),
• BiocManager::repositories(version="3.22") when building/checking a BioC 3.22 package (devel).

[jeroen]

@hpages In the R-universe infrastructure we need a slightly more flexible approach, because it should possible people developing a package in their own universe (outside of bioc) to add a dependency on a useful bioconductor package, without locking themselves into a particular bioc branch and hence limiting their users to the single R version prescribed by bioc.

For this reason (and also because of the range of supported platforms) R-universe gets the dependencies also from R-universe. So if one package has a strict version requirement on another, it is best to put this dependency also in the same universe. Hence indeed, adding a suitable version of Gviz should solve the above problem.

Dependencies that not in the universe itself, are is taken from https://bioc.r-universe.dev/ or https://cran.r-universe.dev. The former indeed contains the latest git versions, so those will probably corresponds to what bioc has in "devel".

As mentioned before, I would really try to encourage package authors to not add too many unnecessary version constraints if possible, because this adds a lot of friction.