Dependency analysis on package biomaRt

General information

Bioconductor link link
Package version2.52.0
Number of strong dependencies70
Number of all dependencies100
Number of parent packages11
Max heaviness from parent packages15
Total heaviness from parent packages36
Number of parent packages (including Suggests and Enhances)16
Max co-heaviness from parent packages ("BiocFileCache" and "AnnotationDbi")11

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils tools stats grDevices graphics stats4 glue R6 magrittr jsonlite rlang pkgconfig vctrs crayon cli stringi ellipsis lifecycle fastmap curl mime openssl askpass sys rappdirs pillar tibble withr fansi utf8 DBI RSQLite bit64 blob memoise Rcpp plogr httr bit cachem hms prettyunits BiocGenerics Biobase IRanges S4Vectors KEGGREST png Biostrings XVector GenomeInfoDb zlibbioc RCurl GenomeInfoDbData bitops dbplyr dplyr filelock assertthat purrr tidyselect generics evaluate digest yaml xfun highr stringr knitr htmltools jquerylib tinytex bslib base64enc sass fs brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 bookdown rmarkdown BiocManager testthat 0 5 10 Imported methods 0 20 40 Required packages 0 5 10 15 Heaviness from parents methods utils rappdirs digest xml2 XML stringr httr progress AnnotationDbi BiocFileCache knitr rmarkdown BiocStyle testthat mockery In total 70 packages are required directly or indirectly (100) when installing 'biomaRt' (2.52.0) Depends Imports Suggests Base packages that are required Contributed packages that are required Packages that are required for installing 'biomaRt' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on biomaRt
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of biomaRt. 0 0
AnnotationDbi Imports 4 0 0 44 15
BiocFileCache Imports 6 0 0 46 13
progress Imports 1 0 0 14 3
stringr Imports 3 0 0 7 2
digest Imports 1 0 0 1 1
xml2 Imports 1 0 0 1 1
XML Imports The whole set of functions/methods/classes from parent package is imported to the namespace of biomaRt. 2 1
utils Imports 3 0 0 0 0
rappdirs Imports 1 0 0 0 0
httr Imports 11 0 0 9 0
BiocStyle Suggests No object is imported into the namespace of biomaRt. 30 16
mockery Suggests No object is imported into the namespace of biomaRt. 37 15
testthat Suggests No object is imported into the namespace of biomaRt. 36 14
rmarkdown Suggests No object is imported into the namespace of biomaRt. 27 13
knitr Suggests No object is imported into the namespace of biomaRt. 12 5

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 biomaRt Co-heaviness as Jaccard coeffcient
AnnotationDbi BiocFileCache 11 0.282

Analysis was done with pkgndep.