as_pkgrefs: Convert Data Structures into Package References

In rang: Reconstructing Reproducible R Computational Environments

Convert Data Structures into Package References

Description

This generic function converts several standard data structures into a vector of package references, which in turn can be used as the first argument of the function resolve(). This function guessimates the possible sources of the packages. But we strongly recommend manually reviewing the detected packages before using them for resolve().

Usage

as_pkgrefs(x, ...)

## Default S3 method:
as_pkgrefs(x, ...)

## S3 method for class 'character'
as_pkgrefs(x, bioc_version = NULL, no_enhances = TRUE, no_suggests = TRUE, ...)

## S3 method for class 'sessionInfo'
as_pkgrefs(x, ...)

Arguments

x,	currently supported data structure(s) are: output from sessionInfo(), a character vector of package names
...,	not used
bioc_version	character. When x is a character vector, version of Bioconductor to search for package names. NULL indicates not search for Bioconductor.
no_enhances	logical, when parsing DESCRIPTION, whether to ignore packages in the "Enhances" field
no_suggests	logical, when parsing DESCRIPTION, whether to ignore packages in the "Suggests" field

Value

a vector of package references

Examples

as_pkgrefs(sessionInfo())
if (interactive()) {
   require(rang)
   graph <- resolve(as_pkgrefs(sessionInfo()))
   as_pkgrefs(c("rtoot"))
   as_pkgrefs(c("rtoot", "S4Vectors")) ## this gives cran::S4Vectors and is not correct.
   as_pkgrefs(c("rtoot", "S4Vectors"), bioc_version = "3.3") ## This gives bioc::S4Vectors
}

rang documentation built on Oct. 8, 2023, 5:06 p.m.