Package: pkgndep 1.99.1

Zuguang Gu

pkgndep: Analyze Dependency Heaviness of R Packages

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 and the results are implemented as a web-based database which provides comprehensive tools for querying dependencies of individual R packages. The systematic analysis on the CRAN/Bioconductor ecosystem is described in <doi:10.1016/j.jss.2023.111610>. From 'pkgndep' version 2.0.0, the heaviness database includes snapshots of the CRAN/Bioconductor ecosystems for many old R versions.

Authors:Zuguang Gu [aut, cre]

pkgndep_1.99.1.tar.gz
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pkgndep.pdf |pkgndep.html✨
pkgndep/json (API)
NEWS

# Install 'pkgndep' in R:
install.packages('pkgndep', repos = c('https://jokergoo.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jokergoo/pkgndep/issues

On CRAN:

6.42 score 45 stars 29 scripts 379 downloads 37 exports 26 dependencies

Last updated 1 years agofrom:66df5ec737. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKNov 21 2024

Exports:ALL_BIOC_RELEASESall_pkg_stat_snapshotcheck_pkgchild_dependencyco_heavinessdependency_databasedependency_heatmapdependency_reportdependency_websitedownstream_dependencyget_all_functions_imported_to_childrengini_indexheavinessheaviness_databaseheaviness_from_upstreamheaviness_on_childrenheaviness_on_downstreamheaviness_reportis_parentis_upstreamload_all_pkg_depload_from_heaviness_dbload_heaviness_timelineload_pkg_dbload_pkg_descriptionload_pkg_downstream_dependency_path_snapshotload_pkg_namespaceload_pkg_stat_snapshotloaded_packagesparent_dependencypkgndeppkgndep_optplot.pkgndepprint.pkgndepreformat_dbrequired_dependency_packagesupstream_dependency

Dependencies:BiocGenericsBiocManagerBiocVersionbrewcirclizeclueclustercodetoolscolorspaceComplexHeatmapcrayondigestdoParallelforeachgenericsGetoptLongGlobalOptionshashIRangesiteratorsmatrixStatspngRColorBrewerrjsonS4Vectorsshape

Check the heaviness of package dependencies

Rendered frompkgndep.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-01-03
Started: 2020-04-23

Co-heaviness of two parent packages

Rendered fromco_heaviness.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-01-04
Started: 2022-02-02

Suggestions for optimizing package dependencies

Rendered fromsuggestions.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-01-04
Started: 2022-02-25

The database of heaviness analysis on the CRAN/Bioconductor ecosystem

Rendered fromdatabase.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2023-01-02
Started: 2022-11-13

Readme and manuals

Help Manual

Help pageTopics
All Bioconductor releasesALL_BIOC_RELEASES
The complete table of dependency heaviness for all CRAN/Bioconductor packagesall_pkg_stat_snapshot
Check whether a package is availablecheck_pkg
Get child dependency for a packagechild_dependency
Co-heaviness for pairs of parent packagesco_heaviness
Database of package dependency heaviness of all R packagesdependency_database
Make the dependency heatmapdependency_heatmap
HTML report for package dependency heaviness analysisdependency_report
Database of package dependency heaviness of all R packagesdependency_website
Get downstream dependency for a packagedownstream_dependency
Get functions that are imported to its child packagesget_all_functions_imported_to_children
Gini indexgini_index
Heaviness from parent packagesheaviness
Database of package dependency heaviness of all R packagesheaviness_database
Heaviness from all upstream packagesheaviness_from_upstream
Heaviness on all child packagesheaviness_on_children
Heaviness on all downstream packagesheaviness_on_downstream
HTML report for package dependency heaviness analysisheaviness_report
Test the parent-child relationshipis_parent
Test upstream-downstream relationshipis_upstream
Load dependency analysis results of all packagesload_all_pkg_dep
Load pre-computed objectsload_from_heaviness_db
Load heaviness statistics at all time pointsload_heaviness_timeline
Load package databaseload_pkg_db
Load DESCRIPTION files of all packagesload_pkg_description
Load downstream dependency paths for all packagesload_pkg_downstream_dependency_path_snapshot
Load NAMESPACE files of all packagesload_pkg_namespace
Load all package dependency statisticsload_pkg_stat_snapshot
Loaded packagesloaded_packages
Get parent dependency for a packageparent_dependency
Package dependency analysispkgndep
Global parameters for pkgndeppkgndep_opt
Make the dependency heatmapplot.pkgndep
Print methodprint.pkgndep
Format the package databasereformat_db
Required dependency packagesrequired_dependency_packages
Get upstream dependency for a packageupstream_dependency