Dependency analysis on package HubPub

General information

Bioconductor link link
Package version1.4.0
Number of strong dependencies80
Number of all dependencies177
Number of parent packages8
Max heaviness from parent packages20
Total heaviness from parent packages31
Number of parent packages (including Suggests and Enhances)14
Max co-heaviness from parent packages ("biocthis" and "usethis")13

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils tools grDevices stats graphics parallel grid stats4 R6 glue magrittr jsonlite rlang digest cli crayon lifecycle yaml httr curl mime openssl askpass sys tibble purrr vctrs ellipsis fansi pillar pkgconfig utf8 fs rappdirs stringr stringi base64enc withr fastmap generics tidyselect desc rprojroot BiocManager xml2 rstudioapi memoise stringdist dplyr Matrix cachem Rcpp lattice clipr gert gh whisker credentials zip gitcreds ini rematch2 aws.signature styler usethis R.cache R.methodsS3 R.oo R.utils clisymbols tidytext SnowballC udapi yesno hunspell janeaustenr tokenizers evaluate highr xfun knitr htmltools bslib jquerylib sass tinytex S4Vectors IRanges GenomicRanges AnnotationHub GenomicFeatures Rsamtools rtracklayer BiocGenerics biocViews BiocCheck graph AnnotationDbi Biobase Biostrings DBI GenomeInfoDb OrganismDbi RSQLite AnnotationForge futile.logger XML RCurl XVector BiocFileCache BiocVersion interactiveDisplayBase BiocIO biomaRt zlibbioc bitops BiocParallel Rhtslib GenomicAlignments restfulr RBGL RUnit codetools KEGGREST GenomeInfoDbData bit64 blob plogr lambda.r futile.options dbplyr filelock shiny DT progress snow BH SummarizedExperiment rjson png bit formatR assertthat httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk hms prettyunits MatrixGenerics DelayedArray lazyeval matrixStats bookdown rmarkdown brio callr pkgload praise processx ps waldo diffobj AnnotationHubData ExperimentHub 0 1 2 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents utils fs BiocManager aws.s3 dplyr usethis biocthis available knitr rmarkdown BiocStyle testthat AnnotationHubData ExperimentHubData In total 80 packages are required directly or indirectly (177) when installing 'HubPub' (1.4.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'HubPub' Imported functions Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on HubPub
available Imports 2 0 0 53 20
biocthis Imports Parent package is listed in Imports of HubPub but no object from parent package is imported. 52 7
aws.s3 Imports 2 0 0 15 4
utils Imports 2 0 0 0 0
fs Imports 1 0 0 1 0
BiocManager Imports 1 0 0 1 0
dplyr Imports 1 0 0 20 0
usethis Imports Parent package is listed in Imports of HubPub but no object from parent package is imported. 36 0
ExperimentHubData Suggests No object is imported into the namespace of HubPub. 133 84
AnnotationHubData Suggests No object is imported into the namespace of HubPub. 131 82
BiocStyle Suggests No object is imported into the namespace of HubPub. 30 12
rmarkdown Suggests No object is imported into the namespace of HubPub. 27 10
testthat Suggests No object is imported into the namespace of HubPub. 36 10
knitr Suggests No object is imported into the namespace of HubPub. 12 4

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 HubPub Co-heaviness as Jaccard coeffcient
usethis biocthis 13 0.65

Analysis was done with pkgndep.