Type:	Package
Title:	Analyze Dependency Heaviness of R Packages
Version:	2.0.0
Date:	2026-04-08
Depends:	R (≥ 4.0.0)
Imports:	ComplexHeatmap (≥ 2.6.0), GetoptLong, GlobalOptions, utils, grid, hash, methods, brew
Suggests:	knitr, rmarkdown, svglite, base64, testthat
Description:	A new metric named 'dependency heaviness' is proposed that measures the number of additional dependency packages that a parent package brings to its child package and are unique to the dependency packages imported by all other parents. The dependency heaviness analysis is visualized by a customized heatmap. The package is described in <doi:10.1093/bioinformatics/btac449>. We have also performed the dependency heaviness analysis on the CRAN/Bioconductor package ecosystem, described in <doi:10.1016/j.jss.2023.111610>.
URL:	https://github.com/jokergoo/pkgndep
VignetteBuilder:	knitr
License:	MIT + file LICENSE
Encoding:	UTF-8
RoxygenNote:	7.3.1
NeedsCompilation:	no
Packaged:	2026-04-08 08:36:17 UTC; guz
Author:	Zuguang Gu [aut, cre]
Maintainer:	Zuguang Gu <guzuguang@suat-sz.edu.cn>
Repository:	CRAN
Date/Publication:	2026-04-08 09:40:08 UTC

Co-heaviness for pairs of parent packages

Description

Co-heaviness for pairs of parent packages

Usage

co_heaviness(x, rel = FALSE, a = 10, jaccard = FALSE)

Arguments

Details

Denote a package as P and its two strong parent packages as A and B, i.e., parent packages in "Depends", "Imports" and "LinkingTo", the co-heaviness for A and B is calculated as follows.

Denote S_A as the set of reduced dependency packages when only moving A to "Suggests" of P, and denote S_B as the set of reduced dependency packages when only moving B to "Suggests" of P, denote S_AB as the set of reduced dependency packages when moving A and B together to "Suggests" of P, the co-heaviness of A, B on P is calculatd as length(setdiff(S_AB, union(S_A, S_B))), which is the number of reduced package only caused by co-action of A and B.

Note the co-heaviness is only calculated for parent packages in "Depends", "Imports" and "LinkingTo".

When jaccard is set to TRUE, the function returns jaccard coeffcient. setdiff(S_AB, union(S_A, S_B)) is actually the set of dependencies imported by and only by two parent packages A and B. Thus the jaccard coeffcient is calculated as length(setdiff(S_AB, union(S_A, S_B)))/length(S_AB).

Examples

## Not run: 
# DESeq version 1.36.0, the dependencies have been changed in later versions.
x = readRDS(system.file("extdata", "DESeq2_dep.rds", package = "pkgndep"))
hm = co_heaviness(x)
ComplexHeatmap::Heatmap(hm)
co_heaviness(x, jaccard = TRUE)

## End(Not run)

Current Bioconductor Version

Description

Current Bioconductor Version

Usage

current_bioc_version()

Details

The version information is from https://bioconductor.org/config.yaml

Heaviness from parent packages

Description

Heaviness from parent packages

Usage

heaviness(x, rel = FALSE, a = 10, only_strong_dep = FALSE)

Arguments

Details

The heaviness from a parent package is calculated as follows: If package B is in the Depends/Imports/LinkingTo fields of package A, which means, package B is necessary for package A, denote v1 as the total numbers of packages required for package A, and v2 as the total number of required packages if moving package B to Suggests (which means, now B is not necessary for A). The absolute measure is simply v1 - v2 and relative measure is (v1 + a)/(v2 + a).

In the second scenario, if B is in the Suggests/Enhances fields of package A, now v2 is the total number of required packages if moving B to Imports, the absolute measure is v2 - v1 and relative measure is (v2 + a)/(v1 + a).

Examples

x = readRDS(system.file("extdata", "ComplexHeatmap_dep.rds", package = "pkgndep"))
heaviness(x)
heaviness(x, rel = TRUE)

HTML report for package dependency heaviness analysis

Description

HTML report for package dependency heaviness analysis

Usage

heaviness_report(pkg, file = NULL)

dependency_report(...)

Arguments

Value

The path of the HTML file of the report.

Examples

if(interactive()) {
    x = readRDS(system.file("extdata", "ComplexHeatmap_dep.rds", package = "pkgndep"))
    heaviness_report(x)
}

Load package database

Description

Load package database

Usage

load_pkg_db(
  lib = .libPaths(),
  bioc_version = pkgndep_opt$bioc_version,
  verbose = TRUE
)

Arguments

Details

It loads the package database from CRAN/Bioconductor and locally installed packages.

The database object internaly is cached for repeated use of other functions in this package.

Package dependency analysis

Description

Package dependency analysis

Usage

pkgndep(
  package,
  lib = .libPaths(),
  bioc_version = pkgndep_opt$bioc_version,
  verbose = TRUE
)

Arguments

Value

A pkgndep object.

Examples

## Not run: 
x = pkgndep("ComplexHeatmap")

## End(Not run)
# The `x` variable generated by `pkgndep()` is already saved in this package.
x = readRDS(system.file("extdata", "ComplexHeatmap_dep.rds", package = "pkgndep"))
x
dependency_heatmap(x)

Global parameters for pkgndep

Description

Global parameters for pkgndep

Usage

pkgndep_opt(..., RESET = FALSE, READ.ONLY = NULL, LOCAL = FALSE, ADD = FALSE)

Arguments

Details

There are following parameters:

• bioc_version The bioconductor version. Use numeric version for devel branch.

Make the dependency heatmap

Description

Make the dependency heatmap

Usage

## S3 method for class 'pkgndep'
plot(x, ...)

dependency_heatmap(
  x,
  pkg_fontsize = 10 * cex,
  title_fontsize = 12 * cex,
  legend_fontsize = 10 * cex,
  fix_size = !dev.interactive(),
  cex = 1,
  help = TRUE,
  file = NULL,
  res = 144
)

Arguments

Details

If fix_size is set to TRUE. The size of the whole plot can be obtained by:

size = dependency_heatmap(x, fix_size = TRUE)

where size is a numeric vector of length two which are the width and height of the whole heatmap. If file argument is set, the size of the figure is automatically calculated.

If there are no dependency packages stored in x, NULL is returned.

Value

A vector of two numeric values (in inches) that correspond to the width and height of the plot.

Print method

Description

Print method

Usage

## S3 method for class 'pkgndep'
print(x, ...)

Arguments

Format the package database

Description

Format the package database

Usage

reformat_db(db, version = NULL)

Arguments

Details

It reformats the data frame of the package database into a pkg_db object.

Value

A pkg_db object. There are the following methods:

• pkg_db$get_meta(package, field = NULL) field can take values in "Package", "Version" and "Repository".

• pkg_db$get_dependency_table(package) Get the dependency table.

• pkg_db$get_rev_dependency_table(package) Get the reverse dependency table.

• pkg_db$package_dependencies(package, recursive = FALSE, reverse = FALSE, which = "strong", simplify = FALSE) All the arguments are the same as in tools::package_dependencies(). Argument simplify controls whether to return a data frame or a simplied vector.

Examples

## Not run: 
db = available.packages()
db2 = reformat_db(db)

## End(Not run)