Dependency analysis on package BiocFileCache

General information

Bioconductor link link
Package version2.4.0
Number of strong dependencies46
Number of all dependencies115
Number of parent packages11
Max heaviness from parent packages8
Total heaviness from parent packages20
Number of parent packages (including Suggests and Enhances)16
Max co-heaviness from parent packages ("dplyr" and "dbplyr")13

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests methods utils tools stats grDevices graphics stats4 parallel grid glue magrittr R6 rlang cli vctrs crayon pkgconfig jsonlite lifecycle pillar tibble ellipsis fansi utf8 fastmap blob DBI purrr tidyselect withr generics assertthat dplyr curl mime openssl askpass sys bit64 memoise Rcpp plogr bit cachem evaluate yaml highr stringr xfun stringi digest knitr htmltools jquerylib tinytex bslib base64enc sass fs rappdirs bookdown rmarkdown BiocManager brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 GenomicRanges XML BiocGenerics S4Vectors IRanges XVector GenomeInfoDb Biostrings zlibbioc RCurl Rsamtools GenomicAlignments BiocIO restfulr GenomeInfoDbData bitops BiocParallel Rhtslib SummarizedExperiment rjson futile.logger snow codetools BH MatrixGenerics Biobase Matrix DelayedArray lambda.r futile.options matrixStats lattice formatR 0 2 4 6 8 Imported methods 0 20 40 Required packages 0 10 20 30 Heaviness from parents dbplyr methods stats utils rappdirs filelock curl DBI httr RSQLite dplyr knitr rmarkdown BiocStyle testthat rtracklayer In total 46 packages are required directly or indirectly (115) when installing 'BiocFileCache' (2.4.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'BiocFileCache' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on BiocFileCache
dbplyr Depends The whole set of functions/methods/classes from parent package is imported to the namespace of BiocFileCache. 28 4
RSQLite Imports The whole set of functions/methods/classes from parent package is imported to the namespace of BiocFileCache. 17 8
httr Imports The whole set of functions/methods/classes from parent package is imported to the namespace of BiocFileCache. 9 6
rappdirs Imports 1 0 0 0 1
filelock Imports 2 0 0 0 1
methods Imports The whole set of functions/methods/classes from parent package is imported to the namespace of BiocFileCache. 0 0
stats Imports 1 0 0 0 0
utils Imports 6 0 0 0 0
curl Imports 1 0 0 0 0
DBI Imports 2 0 0 1 0
dplyr Imports 9 0 0 20 0
rtracklayer Suggests No object is imported into the namespace of BiocFileCache. 44 38
BiocStyle Suggests No object is imported into the namespace of BiocFileCache. 30 19
rmarkdown Suggests No object is imported into the namespace of BiocFileCache. 27 16
testthat Suggests No object is imported into the namespace of BiocFileCache. 36 15
knitr Suggests No object is imported into the namespace of BiocFileCache. 12 7

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 BiocFileCache Co-heaviness as Jaccard coeffcient
dbplyr dplyr 13 0.765

Analysis was done with pkgndep.