Dependency analysis on package RTN

General information

Bioconductor link link
Package version2.20.0
Number of strong dependencies121
Number of all dependencies135
Number of parent packages19
Max heaviness from parent packages60
Total heaviness from parent packages84
Number of parent packages (including Suggests and Enhances)24
Max co-heaviness from parent packages ("car" and "pheatmap")12

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils methods stats graphics grDevices grid tools stats4 splines parallel magrittr Matrix lattice glue BiocGenerics rlang R6 stringr evaluate highr yaml xfun stringi pkgconfig MASS survival nlme knitr digest jsonlite S4Vectors kernlab segmented lifecycle gtable scales farver labeling munsell RColorBrewer viridisLite colorspace Biobase infotheo igraph mixtools e1071 KernSmooth class proxy MatrixGenerics GenomicRanges IRanges GenomeInfoDb DelayedArray matrixStats XVector RCurl GenomeInfoDbData zlibbioc bitops carData abind mgcv nnet pbkrtest quantreg maptools lme4 broom dplyr numDeriv SparseM MatrixModels sp foreign boot minqa nloptr Rcpp RcppEigen backports ellipsis generics purrr tibble tidyr ggplot2 tidyselect vctrs pillar testthat fansi cpp11 isoband withr cli crayon utf8 brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 htmltools jquerylib tinytex bslib base64enc fastmap sass fs rappdirs bookdown rmarkdown BiocManager 0 10 20 Imported methods 0 20 40 60 80 Required packages 0 20 40 60 Heaviness from parents methods stats grDevices graphics utils minet snow data.table pwr limma S4Vectors IRanges igraph RedeR mixtools pheatmap viper SummarizedExperiment car RUnit BiocGenerics knitr rmarkdown BiocStyle In total 121 packages are required directly or indirectly (135) when installing 'RTN' (2.20.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'RTN' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on RTN
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of RTN. 0 0
car Imports 2 0 0 87 60
SummarizedExperiment Imports 3 0 0 24 11
viper Imports 1 0 0 22 5
minet Imports 1 0 0 1 2
snow Imports 5 0 0 1 1
data.table Imports 5 0 0 1 1
pwr Imports 1 0 0 2 1
limma Imports 5 0 0 5 1
RedeR Imports 3 0 0 11 1
pheatmap Imports 1 0 0 18 1
stats Imports 27 0 0 0 0
grDevices Imports 7 0 0 0 0
graphics Imports 21 0 0 0 0
utils Imports 4 0 0 0 0
S4Vectors Imports 2 0 0 6 0
IRanges Imports 5 0 0 7 0
igraph Imports 13 0 0 10 0
mixtools Imports 1 0 0 14 0
BiocStyle Suggests No object is imported into the namespace of RTN. 30 13
rmarkdown Suggests No object is imported into the namespace of RTN. 27 10
RUnit Suggests No object is imported into the namespace of RTN. 3 1
BiocGenerics Suggests No object is imported into the namespace of RTN. 4 0
knitr Suggests No object is imported into the namespace of RTN. 12 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 RTN Co-heaviness as Jaccard coeffcient
pheatmap car 12 0.164

Analysis was done with pkgndep.