Dependency analysis on package mbkmeans

General information

Bioconductor link link
Package version1.12.0
Number of strong dependencies89
Number of all dependencies180
Number of parent packages13
Max heaviness from parent packages19
Total heaviness from parent packages46
Number of parent packages (including Suggests and Enhances)22
Max co-heaviness from parent packages ("ClusterR" and "benchmarkme")14

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests methods utils stats grDevices graphics grid stats4 tools parallel splines compiler lattice Matrix BiocGenerics S4Vectors magrittr MatrixGenerics IRanges matrixStats glue DelayedArray rlang R6 Rcpp pkgconfig digest tibble lifecycle ellipsis fansi pillar vctrs cli crayon utf8 jsonlite codetools GenomicRanges Biobase GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops withr futile.logger snow BH lambda.r futile.options formatR SummarizedExperiment dplyr httr generics tidyselect curl mime openssl purrr askpass sys ggplot2 gtable isoband MASS mgcv scales nlme farver labeling munsell RColorBrewer viridisLite colorspace benchmarkmeData doParallel foreach iterators gtools gmp RcppArmadillo yaml evaluate xfun highr stringr stringi htmltools jquerylib bslib base64enc fastmap sass fs rappdirs sparseMatrixStats rhdf5 rhdf5filters Rhdf5lib BiocNeighbors BiocParallel RcppHNSW knitr tinytex BiocManager SingleCellExperiment cluster igraph bookdown rmarkdown brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 scuttle gridExtra DelayedMatrixStats beachmat BiocSingular ggbeeswarm viridis Rtsne RcppML ggrepel ScaledMatrix irlba rsvd beeswarm vipor RcppEigen HDF5Array AnnotationHub ExperimentHub BiocFileCache RSQLite BiocVersion AnnotationDbi interactiveDisplayBase dbplyr DBI filelock bit64 blob memoise plogr KEGGREST shiny DT assertthat bit cachem png Biostrings httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk lazyeval 0 2 4 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents methods Rcpp S4Vectors Matrix BiocParallel DelayedArray SummarizedExperiment SingleCellExperiment benchmarkme ClusterR Rhdf5lib RcppArmadillo beachmat knitr DelayedMatrixStats HDF5Array bluster rmarkdown BiocStyle testthat scater TENxPBMCData In total 89 packages are required directly or indirectly (180) when installing 'mbkmeans' (1.12.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'mbkmeans' Imported functions 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 mbkmeans.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on mbkmeans
ClusterR Imports The whole set of functions/methods/classes from parent package is imported to the namespace of mbkmeans. 42 19
benchmarkme Imports 1 0 0 41 17
BiocParallel Imports 1 0 0 11 7
SingleCellExperiment Imports 3 0 2 25 1
methods Imports 1 0 0 0 0
Rcpp Imports 1 0 0 2 0
S4Vectors Imports Parent package is listed in Imports of mbkmeans but no object from parent package is imported. 6 0
Matrix Imports 1 0 0 7 0
DelayedArray Imports 3 0 1 14 0
SummarizedExperiment Imports 2 0 1 24 0
Rhdf5lib LinkingTo Parent package is listed in LinkingTo of mbkmeans but no object from parent package is imported. 0 1
beachmat LinkingTo Parent package is listed in LinkingTo of mbkmeans but no object from parent package is imported. 16 1
RcppArmadillo LinkingTo Parent package is listed in LinkingTo of mbkmeans but no object from parent package is imported. 4 0
TENxPBMCData Suggests No object is imported into the namespace of mbkmeans. 100 46
BiocStyle Suggests No object is imported into the namespace of mbkmeans. 30 20
scater Suggests No object is imported into the namespace of mbkmeans. 85 19
rmarkdown Suggests No object is imported into the namespace of mbkmeans. 27 17
testthat Suggests No object is imported into the namespace of mbkmeans. 36 14
knitr Suggests No object is imported into the namespace of mbkmeans. 12 7
bluster Suggests No object is imported into the namespace of mbkmeans. 27 5
HDF5Array Suggests No object is imported into the namespace of mbkmeans. 19 3
DelayedMatrixStats Suggests No object is imported into the namespace of mbkmeans. 17 2

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 mbkmeans Co-heaviness as Jaccard coeffcient
benchmarkme ClusterR 14 0.28

Analysis was done with pkgndep.