Dependency analysis on package AnnotationHubData

General information

Bioconductor link link
Package version1.26.1
Number of strong dependencies131
Number of all dependencies167
Number of parent packages26
Max heaviness from parent packages21
Total heaviness from parent packages29
Number of parent packages (including Suggests and Enhances)33
Max co-heaviness from parent packages ("OrganismDbi" and "GenomicFeatures")6

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils stats graphics stats4 tools grDevices parallel grid BiocGenerics bitops RCurl S4Vectors glue IRanges GenomeInfoDbData GenomeInfoDb XVector zlibbioc yaml jsonlite R6 rlang crayon fastmap Biobase magrittr curl httr memoise pkgconfig Rcpp mime openssl vctrs cli cachem Biostrings askpass sys BiocManager rappdirs DBI bit64 blob plogr bit digest stringr stringi RSQLite KEGGREST png XML BH AnnotationDbi dplyr generics lifecycle tibble tidyselect pillar purrr withr ellipsis fansi utf8 base64enc fs lambda.r futile.options formatR codetools BiocFileCache dbplyr filelock assertthat htmltools bslib jquerylib sass GenomicRanges BiocParallel Rhtslib futile.logger snow evaluate highr xfun Matrix lattice graph RBGL knitr BiocIO Rsamtools GenomicAlignments restfulr SummarizedExperiment rjson MatrixGenerics DelayedArray matrixStats xml2 BiocVersion interactiveDisplayBase shiny DT httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk lazyeval RUnit stringdist rtracklayer biomaRt progress hms prettyunits biocViews GenomicFeatures 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 AnnotationHub 0 5 10 Imported methods 0 50 100 Required packages 0 10 20 30 Heaviness from parents methods utils S4Vectors IRanges GenomicRanges AnnotationHub jsonlite BiocManager DBI XML RCurl BiocGenerics futile.logger Biobase graph GenomeInfoDb biocViews Biostrings RSQLite Rsamtools BiocCheck rtracklayer AnnotationDbi AnnotationForge GenomicFeatures OrganismDbi GenomeInfoDbData RUnit knitr rmarkdown BiocStyle HubPub grasp2db In total 131 packages are required directly or indirectly (167) when installing 'AnnotationHubData' (1.26.1) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'AnnotationHubData' Imported functions Imported S4 methods The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on AnnotationHubData
AnnotationHub Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 85 21
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 0 0
utils Depends 7 0 0 0 0
S4Vectors Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 6 0
IRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 7 0
GenomicRanges Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 15 0
BiocCheck Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 37 6
AnnotationForge Imports 2 0 0 46 1
OrganismDbi Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 100 1
jsonlite Imports 2 0 0 1 0
BiocManager Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 1 0
DBI Imports 0 2 0 1 0
XML Imports 5 0 0 2 0
RCurl Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 2 0
BiocGenerics Imports 0 2 0 4 0
futile.logger Imports 7 0 0 4 0
Biobase Imports 2 0 0 5 0
graph Imports 1 0 0 6 0
GenomeInfoDb Imports 1 0 0 11 0
biocViews Imports 2 0 0 16 0
Biostrings Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 17 0
RSQLite Imports 2 2 0 17 0
Rsamtools Imports 1 1 0 29 0
rtracklayer Imports 2 11 0 44 0
AnnotationDbi Imports 1 3 0 44 0
GenomicFeatures Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHubData. 96 0
HubPub Suggests No object is imported into the namespace of AnnotationHubData. 80 31
BiocStyle Suggests No object is imported into the namespace of AnnotationHubData. 30 4
rmarkdown Suggests No object is imported into the namespace of AnnotationHubData. 27 2
grasp2db Suggests No object is imported into the namespace of AnnotationHubData. 86 1
GenomeInfoDbData Suggests No object is imported into the namespace of AnnotationHubData. 0 0
RUnit Suggests No object is imported into the namespace of AnnotationHubData. 3 0
knitr Suggests No object is imported into the namespace of AnnotationHubData. 12 0

Analysis was done with pkgndep.