Dependency analysis on package topologyGSA

General information

CRAN link link
Package version1.4.7
Number of strong dependencies130
Number of all dependencies130
Number of parent packages5
Max heaviness from parent packages74
Total heaviness from parent packages100
Number of parent packages (including Suggests and Enhances)6
Max co-heaviness from parent packages ("qpgraph" and "fields")14

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods stats utils graphics stats4 grid grDevices splines parallel tools BiocGenerics graph magrittr Matrix pkgconfig lattice Rgraphviz Rcpp BH R6 crayon digest rlang vctrs glue cli ellipsis lifecycle pillar tibble withr fansi utf8 BiocManager RBGL igraph RcppEigen RcppArmadillo spam viridis maps dotCall64 viridisLite ggplot2 gridExtra gtable isoband MASS mgcv scales nlme farver labeling munsell RColorBrewer colorspace annotate Biobase S4Vectors BiocParallel AnnotationDbi IRanges GenomeInfoDb GenomicRanges GenomicFeatures mvtnorm qtl XML DBI xtable httr futile.logger snow codetools RSQLite KEGGREST RCurl GenomeInfoDbData XVector Biostrings BiocIO rtracklayer biomaRt curl jsonlite mime openssl lambda.r futile.options bit64 blob memoise plogr png bitops zlibbioc Rsamtools GenomicAlignments restfulr progress stringr BiocFileCache rappdirs xml2 askpass formatR bit cachem Rhtslib SummarizedExperiment rjson yaml hms prettyunits stringi dbplyr dplyr filelock sys fastmap MatrixGenerics DelayedArray assertthat purrr tidyselect generics matrixStats 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 60 Heaviness from parents methods graph gRbase fields qpgraph Rgraphviz In total 130 packages are required directly or indirectly (130) when installing 'topologyGSA' (1.4.7) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'topologyGSA' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on topologyGSA
qpgraph Imports The whole set of functions/methods/classes from parent package is imported to the namespace of topologyGSA. 103 74
fields Imports The whole set of functions/methods/classes from parent package is imported to the namespace of topologyGSA. 43 20
gRbase Imports The whole set of functions/methods/classes from parent package is imported to the namespace of topologyGSA. 21 6
methods Imports 1 0 0 0 0
graph Imports The whole set of functions/methods/classes from parent package is imported to the namespace of topologyGSA. 6 0
Rgraphviz Suggests No object is imported into the namespace of topologyGSA. 9 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 topologyGSA Co-heaviness as Jaccard coeffcient
fields qpgraph 14 0.13

Analysis was done with pkgndep.