Dependency analysis on package ExperimentHub

General information

Bioconductor link link
Package version2.4.0
Number of strong dependencies86
Number of all dependencies169
Number of parent packages9
Max heaviness from parent packages35
Total heaviness from parent packages35
Number of parent packages (including Suggests and Enhances)14
Max co-heaviness from parent packages ("AnnotationHub" and "BiocFileCache")41

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances utils methods stats tools graphics grDevices stats4 parallel grid glue magrittr rappdirs jsonlite R6 rlang fastmap yaml digest base64enc fs curl httr dplyr memoise pkgconfig Rcpp mime openssl generics lifecycle tibble tidyselect vctrs pillar cli purrr withr cachem crayon ellipsis askpass fansi utf8 sys BiocManager htmltools bslib jquerylib sass RSQLite dbplyr DBI filelock bit64 blob plogr assertthat bit BiocGenerics BiocFileCache BiocVersion AnnotationDbi S4Vectors interactiveDisplayBase Biobase IRanges KEGGREST shiny DT png Biostrings httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk XVector GenomeInfoDb lazyeval zlibbioc RCurl GenomeInfoDbData bitops stringr stringi evaluate highr xfun knitr tinytex stringdist xml2 Matrix lattice bookdown rmarkdown available usethis biocthis aws.s3 clisymbols tidytext desc SnowballC udapi yesno clipr gert gh rprojroot rstudioapi whisker styler aws.signature hunspell janeaustenr tokenizers credentials zip gitcreds ini R.cache rematch2 R.methodsS3 R.oo R.utils AnnotationHubData ExperimentHub GenomicRanges AnnotationHub GenomicFeatures Rsamtools rtracklayer biocViews BiocCheck graph OrganismDbi AnnotationForge futile.logger XML BiocIO biomaRt BiocParallel Rhtslib GenomicAlignments restfulr RBGL RUnit codetools lambda.r futile.options progress snow BH SummarizedExperiment rjson formatR hms prettyunits MatrixGenerics DelayedArray matrixStats 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents methods BiocGenerics BiocFileCache AnnotationHub utils curl rappdirs BiocManager S4Vectors knitr rmarkdown BiocStyle HubPub ExperimentHubData In total 86 packages are required directly or indirectly (169) when installing 'ExperimentHub' (2.4.0) 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 'ExperimentHub' Imported functions 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 ExperimentHub.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ExperimentHub
AnnotationHub Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHub. 85 35
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHub. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHub. 4 0
BiocFileCache Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHub. 46 0
utils Imports 1 0 0 0 0
curl Imports Parent package is listed in Imports of ExperimentHub but no object from parent package is imported. 0 0
rappdirs Imports 1 0 0 0 0
BiocManager Imports 1 0 0 1 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHub. 6 0
HubPub Suggests No object is imported into the namespace of ExperimentHub. 80 39
BiocStyle Suggests No object is imported into the namespace of ExperimentHub. 30 10
rmarkdown Suggests No object is imported into the namespace of ExperimentHub. 27 8
knitr Suggests No object is imported into the namespace of ExperimentHub. 12 6
ExperimentHubData Enhances No object is imported into the namespace of ExperimentHub. 133 48

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 ExperimentHub Co-heaviness as Jaccard coeffcient
BiocFileCache AnnotationHub 41 0.539

Analysis was done with pkgndep.