Dependency analysis on package HDF5Array

General information

Bioconductor link link
Package version1.24.1
Number of strong dependencies19
Number of all dependencies136
Number of parent packages12
Max heaviness from parent packages3
Total heaviness from parent packages5
Number of parent packages (including Suggests and Enhances)22
Max co-heaviness from parent packages ("Matrix" and "DelayedArray")4

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of HDF5Array 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 HDF5Array.

Adjust heatmap size:
Base packages Other packages Depends Imports LinkingTo Suggests methods utils stats graphics stats4 grDevices grid tools parallel BiocGenerics S4Vectors IRanges lattice Matrix MatrixGenerics matrixStats Rhdf5lib rhdf5filters GenomeInfoDb XVector RCurl GenomeInfoDbData zlibbioc bitops Biobase GenomicRanges DelayedArray SummarizedExperiment rappdirs filelock Rcpp jsonlite glue cli withr png BiocFileCache curl RSQLite AnnotationDbi httr yaml dplyr dbplyr DBI bit64 blob memoise pkgconfig plogr KEGGREST mime openssl R6 generics lifecycle magrittr rlang tibble tidyselect vctrs pillar assertthat purrr bit cachem Biostrings crayon fastmap ellipsis askpass fansi utf8 digest sys futile.logger snow codetools BH lambda.r futile.options formatR SingleCellExperiment AnnotationHub BiocManager BiocVersion interactiveDisplayBase shiny DT httpuv xtable fontawesome htmltools sourcetools later promises commonmark bslib htmlwidgets crosstalk jquerylib base64enc sass lazyeval fs basilisk reticulate dir.expiry basilisk.utils RcppTOML here rprojroot BiocIO rtracklayer biomaRt XML Rsamtools GenomicAlignments restfulr progress stringr xml2 BiocParallel Rhtslib rjson hms prettyunits stringi HDF5Array ExperimentHub rhdf5 0 0.5 1 Imported methods 0 50 100 Required packages 0 20 40 60 80 Heaviness from parents methods rhdf5 DelayedArray utils stats tools rhdf5filters BiocGenerics S4Vectors Matrix IRanges Rhdf5lib h5vcData RUnit BiocParallel GenomicRanges SummarizedExperiment SingleCellExperiment zellkonverter ExperimentHub GenomicFeatures TENxBrainData In total 19 packages are required directly or indirectly (136) when installing 'HDF5Array' (1.24.1) Depends Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'HDF5Array' Imported functions 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 HDF5Array.

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 HDF5Array: number of required packages that can be reduced if moving parent package to Suggests of HDF5Array.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on HDF5Array
DelayedArray Depends The whole set of functions/methods/classes from parent package is imported to the namespace of HDF5Array. 14 3
rhdf5 Depends The whole set of functions/methods/classes from parent package is imported to the namespace of HDF5Array. 3 1
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of HDF5Array. 0 0
tools Imports 1 0 0 0 1
utils Imports 1 0 0 0 0
stats Imports 1 0 0 0 0
rhdf5filters Imports The whole set of functions/methods/classes from parent package is imported to the namespace of HDF5Array. 1 0
BiocGenerics Imports The whole set of functions/methods/classes from parent package is imported to the namespace of HDF5Array. 4 0
S4Vectors Imports The whole set of functions/methods/classes from parent package is imported to the namespace of HDF5Array. 6 0
Matrix Imports 1 0 0 7 0
IRanges Imports The whole set of functions/methods/classes from parent package is imported to the namespace of HDF5Array. 7 0
Rhdf5lib LinkingTo Parent package is listed in LinkingTo of HDF5Array but no object from parent package is imported. 0 0
TENxBrainData Suggests No object is imported into the namespace of HDF5Array. 100 82
GenomicFeatures Suggests No object is imported into the namespace of HDF5Array. 96 81
ExperimentHub Suggests No object is imported into the namespace of HDF5Array. 86 77
zellkonverter Suggests No object is imported into the namespace of HDF5Array. 42 27
SingleCellExperiment Suggests No object is imported into the namespace of HDF5Array. 25 10
BiocParallel Suggests No object is imported into the namespace of HDF5Array. 11 9
SummarizedExperiment Suggests No object is imported into the namespace of HDF5Array. 24 9
GenomicRanges Suggests No object is imported into the namespace of HDF5Array. 15 7
h5vcData Suggests No object is imported into the namespace of HDF5Array. 0 1
RUnit Suggests No object is imported into the namespace of HDF5Array. 3 1

Analysis was done with pkgndep.