Dependency analysis on package keggorthology

General information

Bioconductor link link
Package version2.48.0
Number of strong dependencies48
Number of all dependencies51
Number of parent packages9
Max heaviness from parent packages2
Total heaviness from parent packages3
Number of parent packages (including Suggests and Enhances)11
Max co-heaviness from parent packages ("AnnotationDbi" and "hgu95av2.db")36

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of keggorthology and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on keggorthology.

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods stats utils graphics stats4 grDevices tools BiocGenerics Biobase IRanges DBI RSQLite S4Vectors KEGGREST bit64 blob memoise pkgconfig Rcpp plogr httr png Biostrings bit rlang vctrs cachem curl jsonlite mime openssl R6 XVector GenomeInfoDb crayon cli glue fastmap askpass zlibbioc RCurl GenomeInfoDbData sys bitops AnnotationDbi org.Hs.eg.db graph BH 0 10 20 Imported methods 0 20 40 Required packages 0 1 2 Heaviness from parents stats graph hgu95av2.db grDevices methods tools utils DBI AnnotationDbi ALL RBGL In total 48 packages are required directly or indirectly (51) when installing 'keggorthology' (2.48.0) Depends Imports Suggests Base packages that are required Contributed packages that are required Packages that are required for installing 'keggorthology' Imported functions Imported S4 methods Package is listed in 'Imports' but namespace is not imported


Dependency table

"Import" information is from the NAMESPACE file of keggorthology.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on keggorthology: number of required packages that can be reduced if moving parent package to Suggests of keggorthology.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on keggorthology
hgu95av2.db Depends Parent package is listed in Depends of keggorthology but no object from parent package is imported. 46 2
graph Depends 0 12 0 6 1
stats Depends 26 0 0 0 0
grDevices Imports 1 0 0 0 0
methods Imports 3 0 0 0 0
tools Imports 1 0 0 0 0
utils Imports 5 0 0 0 0
DBI Imports Parent package is listed in Imports of keggorthology but no object from parent package is imported. 1 0
AnnotationDbi Imports 0 5 0 44 0
RBGL Suggests No object is imported into the namespace of keggorthology. 8 2
ALL Suggests No object is imported into the namespace of keggorthology. 6 1

The following table lists pairs of parent packages with co-heaviness larger than 10. The co-heaviness measures the number of additional dependencies that two parent packages simultaneously import and are only imported by the two parents.

Note the co-heaviness from parents can be always easily observed in the dependency heatmap.

Parent 1 Parent 2 Co-heaviness on keggorthology Co-heaviness as Jaccard coeffcient
hgu95av2.db AnnotationDbi 36 0.947

Analysis was done with pkgndep.