buildPkgDependencyDataFrame: Work with Bioconductor package dependencies

In seandavi/BiocPkgTools: Collection of simple tools for learning about Bioconductor Packages

Work with Bioconductor package dependencies

Description

Bioconductor is built using an extensive set of core capabilities and data structures. This leads to package developers depending on other packages for interoperability and functionality. This function extracts package dependency information from biocPkgList and returns a tidy data.frame that can be used for analysis and to build graph structures of package dependencies.

Usage

buildPkgDependencyDataFrame(dependencies = c("strong", "most", "all"), ...)

Arguments

dependencies	character() a vector listing the types of dependencies, a subset of c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances"). Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector.
...	parameters passed along to biocPkgList

Value

A data.frame (also a tbl_df) of S3 class "biocDepDF" including columns "Package", "dependency", and "edgetype".

Note

This function requires network access.

See Also

See buildPkgDependencyIgraph, biocPkgList.

Examples

# performs a network call, so must be online.
library(BiocPkgTools)
depdf <- buildPkgDependencyDataFrame()
head(depdf)
library(dplyr)
# filter to include only "Imports" type
# dependencies
imports_only <- depdf |> filter(edgetype=='Imports')

# top ten most imported packages
imports_only |> select(dependency) |>
  group_by(dependency) |> tally() |>
  arrange(desc(n))

# The Bioconductor packages with the
# largest number of imports
largest_importers <- imports_only |>
  select(Package) |>
  group_by(Package) |> tally() |>
  arrange(desc(n))

# not sure what these packages do. Join
# to their descriptions
biocPkgList() |> select(Package, Description) |>
  left_join(largest_importers) |> arrange(desc(n)) |>
  head()

seandavi/BiocPkgTools documentation built on May 23, 2024, 1:53 p.m.