Dependency analysis on package VanillaICE

General information

Bioconductor link link
Package version1.58.0
Number of strong dependencies83
Number of all dependencies96
Number of parent packages20
Max heaviness from parent packages18
Total heaviness from parent packages33
Number of parent packages (including Suggests and Enhances)27
Max co-heaviness from parent packages ("crlmm" and "oligoClasses")19

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances utils methods graphics stats stats4 tools grid grDevices parallel splines compiler BiocGenerics codetools iterators S4Vectors foreach IRanges RCurl GenomeInfoDbData bitops GenomeInfoDb XVector zlibbioc matrixStats MatrixGenerics GenomicRanges Biobase Matrix DelayedArray lattice SummarizedExperiment Biostrings crayon snow affyio BiocManager RSQLite DBI ff bit64 blob memoise pkgconfig Rcpp plogr bit rlang vctrs cachem cli glue fastmap BSgenome rtracklayer Rsamtools XML GenomicAlignments BiocIO restfulr BiocParallel Rhtslib rjson yaml futile.logger BH lambda.r futile.options formatR oligoClasses preprocessCore illuminaio ellipse mvtnorm RcppEigen VGAM limma beanplot base64 openssl askpass sys Rmpi redux R6 storr digest 0 5 10 Imported methods 0 20 40 60 Required packages 0 5 10 15 Heaviness from parents BiocGenerics GenomicRanges SummarizedExperiment matrixStats grid methods tools stats utils data.table MatrixGenerics foreach Biobase lattice S4Vectors IRanges GenomeInfoDb BSgenome.Hsapiens.UCSC.hg18 oligoClasses crlmm human610quadv1bCrlmm RUnit doMC doSNOW doParallel doMPI doRedis In total 83 packages are required directly or indirectly (96) when installing 'VanillaICE' (1.58.0) Depends Imports Suggests Enhances Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'VanillaICE' Imported functions Imported S4 methods 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 VanillaICE.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on VanillaICE
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 4 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 15 0
SummarizedExperiment Depends The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 24 0
BSgenome.Hsapiens.UCSC.hg18 Imports Parent package is listed in Imports of VanillaICE but no object from parent package is imported. 46 18
crlmm Imports 1 0 0 63 14
data.table Imports 1 0 0 1 1
matrixStats Imports 2 0 0 0 0
grid Imports The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 0 0
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 0 0
tools Imports 1 0 0 0 0
stats Imports 7 0 0 0 0
utils Imports 2 0 0 0 0
MatrixGenerics Imports Parent package is listed in Imports of VanillaICE but no object from parent package is imported. 2 0
foreach Imports The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 3 0
Biobase Imports 4 8 0 5 0
lattice Imports The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 5 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 6 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 7 0
GenomeInfoDb Imports The whole set of functions/methods/classes from parent package is imported to the namespace of VanillaICE. 11 0
oligoClasses Imports 2 4 0 48 0
human610quadv1bCrlmm Suggests No object is imported into the namespace of VanillaICE. 1 1
RUnit Suggests No object is imported into the namespace of VanillaICE. 3 1
doRedis Enhances No object is imported into the namespace of VanillaICE. 9 5
doMPI Enhances No object is imported into the namespace of VanillaICE. 7 3
doMC Enhances No object is imported into the namespace of VanillaICE. 5 1
doSNOW Enhances No object is imported into the namespace of VanillaICE. 5 1
doParallel Enhances No object is imported into the namespace of VanillaICE. 5 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 VanillaICE Co-heaviness as Jaccard coeffcient
oligoClasses crlmm 19 0.576

Analysis was done with pkgndep.