Dependency analysis on package bumphunter

General information

Bioconductor link link
Package version1.38.0
Number of strong dependencies103
Number of all dependencies121
Number of parent packages17
Max heaviness from parent packages45
Total heaviness from parent packages49
Number of parent packages (including Suggests and Enhances)22
Max co-heaviness from parent packages ("GenomicFeatures" and "AnnotationDbi")29

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics stats4 grDevices tools parallel grid BiocGenerics S4Vectors IRanges RCurl GenomeInfoDbData bitops codetools GenomeInfoDb XVector zlibbioc pkgconfig crayon rlang vctrs R6 glue jsonlite cli digest DBI RSQLite Biostrings Biobase KEGGREST bit64 blob memoise Rcpp plogr httr png bit cachem curl mime openssl fastmap askpass sys iterators lattice AnnotationDbi magrittr ellipsis lifecycle pillar tibble withr fansi utf8 foreach GenomicRanges BiocIO rtracklayer biomaRt XML Rsamtools GenomicAlignments restfulr progress stringr BiocFileCache rappdirs xml2 BiocParallel Rhtslib SummarizedExperiment rjson yaml hms prettyunits stringi dbplyr dplyr filelock futile.logger snow BH MatrixGenerics Matrix DelayedArray assertthat purrr tidyselect generics lambda.r futile.options matrixStats formatR rngtools brio callr desc evaluate pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 GenomicFeatures 0 10 20 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents methods parallel iterators foreach S4Vectors locfit IRanges GenomeInfoDb GenomicRanges matrixStats utils stats BiocGenerics limma doRNG AnnotationDbi GenomicFeatures RUnit doParallel testthat org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene In total 103 packages are required directly or indirectly (121) when installing 'bumphunter' (1.38.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'bumphunter' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on bumphunter
locfit Depends 2 0 0 6 1
methods Depends 1 0 1 0 0
parallel Depends 2 0 0 0 0
iterators Depends 1 0 0 1 0
foreach Depends 7 0 0 3 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of bumphunter. 6 0
IRanges Depends 3 18 0 7 0
GenomeInfoDb Depends 1 0 0 11 0
GenomicRanges Depends 2 1 0 15 0
GenomicFeatures Imports 3 0 0 96 45
doRNG Imports 1 0 0 9 2
limma Imports Parent package is listed in Imports of bumphunter but no object from parent package is imported. 5 1
matrixStats Imports The whole set of functions/methods/classes from parent package is imported to the namespace of bumphunter. 0 0
utils Imports 2 0 0 0 0
stats Imports 3 0 0 0 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of bumphunter. 4 0
AnnotationDbi Imports 1 1 0 44 0
testthat Suggests No object is imported into the namespace of bumphunter. 36 14
RUnit Suggests No object is imported into the namespace of bumphunter. 3 1
doParallel Suggests No object is imported into the namespace of bumphunter. 5 1
org.Hs.eg.db Suggests No object is imported into the namespace of bumphunter. 45 1
TxDb.Hsapiens.UCSC.hg19.knownGene Suggests No object is imported into the namespace of bumphunter. 97 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 bumphunter Co-heaviness as Jaccard coeffcient
AnnotationDbi GenomicFeatures 29 0.392

Analysis was done with pkgndep.