Dependency analysis on package AnnotationHub

General information

Bioconductor link link
Package version3.4.0
Number of strong dependencies85
Number of all dependencies208
Number of parent packages16
Max heaviness from parent packages20
Total heaviness from parent packages38
Number of parent packages (including Suggests and Enhances)37
Max co-heaviness from parent packages ("dplyr" and "BiocFileCache")8

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests Enhances methods utils stats graphics tools grDevices stats4 grid parallel splines BiocGenerics glue R6 rlang crayon S4Vectors IRanges magrittr Rcpp jsonlite fastmap zlibbioc RCurl GenomeInfoDbData bitops cli vctrs pkgconfig XVector GenomeInfoDb mime cachem yaml Biobase rappdirs curl lifecycle memoise openssl ellipsis askpass sys digest DBI httr blob pillar tibble withr bit64 plogr fansi utf8 bit Biostrings RSQLite purrr tidyselect generics dplyr base64enc fs KEGGREST png dbplyr filelock assertthat htmltools bslib jquerylib sass shiny DT httpuv xtable fontawesome sourcetools later promises commonmark htmlwidgets crosstalk lazyeval XML stringr stringi Matrix lattice GenomicRanges BiocParallel futile.logger snow codetools BH lambda.r futile.options formatR MatrixGenerics matrixStats DelayedArray Rhtslib BiocManager AnnotationDbi xfun evaluate highr SummarizedExperiment Rsamtools GenomicAlignments BiocIO restfulr rjson xml2 BiocFileCache knitr rtracklayer biomaRt progress hms prettyunits ProtGenerics ncdf4 Rhdf5lib tinytex stringdist AnnotationHub BiocVersion interactiveDisplayBase GenomicFeatures data.table bookdown rmarkdown mzR MsCoreUtils plyr vsn affy impute pcaMethods MALDIquant mzID ggplot2 scales MASS clue limma affyio preprocessCore doParallel foreach iterators gtable isoband mgcv farver labeling munsell RColorBrewer viridisLite cluster nlme colorspace 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 BSgenome biocViews BiocCheck graph OrganismDbi AnnotationForge RBGL RUnit 0 5 10 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents BiocGenerics BiocFileCache utils methods grDevices BiocVersion curl rappdirs yaml BiocManager S4Vectors httr RSQLite dplyr interactiveDisplayBase AnnotationDbi gdsfmt RUnit rBiopaxParser IRanges mzR GenomeInfoDb knitr GenomicRanges Biostrings SummarizedExperiment rmarkdown Rsamtools BiocStyle rtracklayer AnnotationForge MSnbase HubPub ExperimentHub GenomicFeatures VariantAnnotation AnnotationHubData In total 85 packages are required directly or indirectly (208) when installing 'AnnotationHub' (3.4.0) 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 'AnnotationHub' Imported functions Imported S4 methods 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 AnnotationHub.

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on AnnotationHub
BiocFileCache Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHub. 46 4
BiocGenerics Depends The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHub. 4 0
interactiveDisplayBase Imports 1 0 0 41 20
AnnotationDbi Imports 1 2 0 44 12
BiocVersion Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHub. 0 1
BiocManager Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHub. 1 1
utils Imports 7 0 0 0 0
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHub. 0 0
grDevices Imports 1 0 0 0 0
curl Imports Parent package is listed in Imports of AnnotationHub but no object from parent package is imported. 0 0
rappdirs Imports 1 0 0 0 0
yaml Imports 1 0 0 0 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHub. 6 0
httr Imports 10 0 0 9 0
RSQLite Imports The whole set of functions/methods/classes from parent package is imported to the namespace of AnnotationHub. 17 0
dplyr Imports 2 0 0 20 0
MSnbase Suggests No object is imported into the namespace of AnnotationHub. 76 48
HubPub Suggests No object is imported into the namespace of AnnotationHub. 80 39
VariantAnnotation Suggests No object is imported into the namespace of AnnotationHub. 98 35
GenomicFeatures Suggests No object is imported into the namespace of AnnotationHub. 96 33
rtracklayer Suggests No object is imported into the namespace of AnnotationHub. 44 25
Rsamtools Suggests No object is imported into the namespace of AnnotationHub. 29 12
BiocStyle Suggests No object is imported into the namespace of AnnotationHub. 30 10
SummarizedExperiment Suggests No object is imported into the namespace of AnnotationHub. 24 8
rmarkdown Suggests No object is imported into the namespace of AnnotationHub. 27 8
knitr Suggests No object is imported into the namespace of AnnotationHub. 12 6
mzR Suggests No object is imported into the namespace of AnnotationHub. 10 4
rBiopaxParser Suggests No object is imported into the namespace of AnnotationHub. 4 3
AnnotationForge Suggests No object is imported into the namespace of AnnotationHub. 46 2
ExperimentHub Suggests No object is imported into the namespace of AnnotationHub. 86 2
gdsfmt Suggests No object is imported into the namespace of AnnotationHub. 1 1
RUnit Suggests No object is imported into the namespace of AnnotationHub. 3 1
GenomicRanges Suggests No object is imported into the namespace of AnnotationHub. 15 1
IRanges Suggests No object is imported into the namespace of AnnotationHub. 7 0
GenomeInfoDb Suggests No object is imported into the namespace of AnnotationHub. 11 0
Biostrings Suggests No object is imported into the namespace of AnnotationHub. 17 0
AnnotationHubData Enhances No object is imported into the namespace of AnnotationHub. 131 47

Analysis was done with pkgndep.