Dependency analysis on package ExperimentHubData

General information

Bioconductor link link
Package version1.22.0
Number of strong dependencies133
Number of all dependencies168
Number of parent packages10
Max heaviness from parent packages46
Total heaviness from parent packages47
Number of parent packages (including Suggests and Enhances)16
Max co-heaviness from parent packages ("ExperimentHub" and "AnnotationHubData")68

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics tools grDevices stats4 parallel grid jsonlite yaml R6 glue magrittr rappdirs rlang stringr digest fastmap stringi base64enc fs BiocGenerics BiocManager curl mime openssl evaluate highr xfun htmltools bslib jquerylib askpass sass sys S4Vectors IRanges RCurl httr dplyr bitops knitr crayon GenomeInfoDbData memoise pkgconfig Rcpp generics lifecycle tibble tidyselect vctrs pillar cachem cli purrr withr ellipsis fansi utf8 AnnotationHub AnnotationDbi Biobase Biostrings DBI GenomeInfoDb RSQLite XVector BiocFileCache BiocVersion interactiveDisplayBase zlibbioc stringdist KEGGREST bit64 blob plogr dbplyr filelock shiny DT xml2 png bit assertthat httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk Matrix lazyeval lattice GenomicRanges 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 tinytex 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 0 1 2 3 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents utils BiocGenerics S4Vectors AnnotationHubData methods curl BiocManager DBI httr ExperimentHub RUnit GenomeInfoDb knitr rmarkdown BiocStyle HubPub In total 133 packages are required directly or indirectly (168) when installing 'ExperimentHubData' (1.22.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'ExperimentHubData' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on ExperimentHubData
AnnotationHubData Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHubData. 131 46
utils Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHubData. 0 0
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHubData. 4 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHubData. 6 0
ExperimentHub Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHubData. 86 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHubData. 0 0
curl Imports 3 0 0 0 0
BiocManager Imports 1 0 0 1 0
DBI Imports 2 0 0 1 0
httr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of ExperimentHubData. 9 0
HubPub Suggests No object is imported into the namespace of ExperimentHubData. 80 31
BiocStyle Suggests No object is imported into the namespace of ExperimentHubData. 30 4
rmarkdown Suggests No object is imported into the namespace of ExperimentHubData. 27 2
RUnit Suggests No object is imported into the namespace of ExperimentHubData. 3 0
GenomeInfoDb Suggests No object is imported into the namespace of ExperimentHubData. 11 0
knitr Suggests No object is imported into the namespace of ExperimentHubData. 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 ExperimentHubData Co-heaviness as Jaccard coeffcient
AnnotationHubData ExperimentHub 68 0.591

Analysis was done with pkgndep.