resolve: Resolve Dependencies Of R Packages

Description

This function recursively queries dependencies of R packages at a specific snapshot time. The dependency graph can then be used to recreate the computational environment. The data on dependencies are provided by R-hub.

Usage

resolve(
  pkgs = ".",
  snapshot_date,
  no_enhances = TRUE,
  no_suggests = TRUE,
  query_sysreqs = TRUE,
  os = "ubuntu-20.04",
  verbose = FALSE
)

Value

a rang S3 object with the following items

call: original function call
ranglets: List of dependency graphs of all packages in pkgs
snapshot_date: snapshot_date
no_enhances: no_enhances
no_suggests: no_suggests
unresolved_pkgsrefs: Packages that can't be resolved
sysreqs: System requirements as Linux commands
r_version: The latest R version as of snapshot_date
os: os

Arguments

pkgs: pkgs can be 1) a character vector of R packages to resolve, 2) a path to a renv lockfile, or 3) a data structure that as_pkgrefs() can convert to a character vector of package references. For 1) pkgs can be either in shorthands, e.g. "rtoot", "ropensci/readODS", or in package references, e.g. "cran::rtoot", "github::ropensci/readODS". Please refer to the Package References documentation of pak for details. Currently, this package supports only cran and github packages. For 2) as_pkgrefs() support the output of sessionInfo(), a renv lockfile or a single directory. If it is a single directory, all R scripts are scanned for R packages used using renv::dependencies(). Currently, the default is to scan the R scripts in the current working directory. Please also note that this scanning only assumes there are CRAN and Bioconductor packages. We strongly recommend checking whether this is really the case (see example below).
snapshot_date: Snapshot date, if not specified, assume to be a month ago
no_enhances: logical, whether to ignore packages in the "Enhances" field
no_suggests: logical, whether to ignore packages in the "Suggests" field
query_sysreqs: logical, whether to query for System Requirements. Important: Archived CRAN can't be queried for system requirements. Those packages are assumed to have no system requirement.
os: character, which OS to query for system requirements
verbose: logical, whether to display messages

References

Package References

Examples

Run this code

# \donttest{
if (interactive()) {
    graph <- resolve(pkgs = c("openNLP", "LDAvis", "topicmodels", "quanteda"),
                snapshot_date = "2020-01-16")
    graph
    ## to resolve github packages
    gh_graph <- resolve(pkgs = c("https://github.com/schochastics/rtoot"),
                   snapshot_date = "2022-11-28")
    gh_graph
    ## scanning
    graph <- resolve(snapshot_date = "2022-11-28")
    ## But we recommend this:
    pkgs <- as_pkgrefs(".")
    pkgs ## check the accuracy
    graph <- resolve(pkgs, snapshot_date = "2022-11-28")
}
# }