Dependency analysis on package pdInfoBuilder

General information

Bioconductor link link
Package version1.60.0
Number of strong dependencies53
Number of all dependencies53
Number of parent packages11
Max heaviness from parent packages3
Total heaviness from parent packages3
Number of parent packages (including Suggests and Enhances)11
Max co-heaviness from parent packages ("oligoClasses" and "oligo")15

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of pdInfoBuilder 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 pdInfoBuilder.

Adjust heatmap size:
Base packages Other packages Depends Imports methods utils stats graphics stats4 grDevices tools grid splines BiocGenerics S4Vectors bit64 blob DBI memoise pkgconfig Rcpp plogr bit rlang vctrs cachem cli glue fastmap zlibbioc IRanges XVector GenomeInfoDb crayon RCurl GenomeInfoDbData bitops Biobase Biostrings affyio ff RSQLite GenomicRanges SummarizedExperiment foreach BiocManager MatrixGenerics Matrix DelayedArray codetools iterators matrixStats lattice oligoClasses affxparser preprocessCore 0 5 10 Imported methods 0 20 40 Required packages 0 1 2 3 Heaviness from parents methods affxparser Biobase RSQLite oligo DBI BiocGenerics S4Vectors IRanges Biostrings oligoClasses In total 53 packages are required directly or indirectly (53) when installing 'pdInfoBuilder' (1.60.0) Depends Imports Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'pdInfoBuilder' Imported functions Imported S4 methods Imported S4 classes Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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 pdInfoBuilder: number of required packages that can be reduced if moving parent package to Suggests of pdInfoBuilder.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on pdInfoBuilder
oligo Depends 1 0 0 52 3
methods Depends 3 1 0 0 0
affxparser Depends 9 0 0 0 0
Biobase Depends 1 0 1 5 0
RSQLite Depends 1 10 0 17 0
DBI Imports 0 1 0 1 0
BiocGenerics Imports Parent package is listed in Imports of pdInfoBuilder but no object from parent package is imported. 4 0
S4Vectors Imports 1 0 0 6 0
IRanges Imports Parent package is listed in Imports of pdInfoBuilder but no object from parent package is imported. 7 0
Biostrings Imports 1 0 0 17 0
oligoClasses Imports Parent package is listed in Imports of pdInfoBuilder but no object from parent package is imported. 48 0

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 pdInfoBuilder Co-heaviness as Jaccard coeffcient
oligo oligoClasses 15 0.833

Analysis was done with pkgndep.