Dependency analysis on package GSVAdata

General information

Bioconductor link link
Package version1.32.0
Number of strong dependencies52
Number of all dependencies52
Number of parent packages3
Max heaviness from parent packages5
Total heaviness from parent packages7
Number of parent packages (including Suggests and Enhances)3
Max co-heaviness from parent packages ("GSEABase" and "hgu95a.db")39

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends utils methods graphics stats stats4 tools grDevices BiocGenerics Biobase AnnotationDbi DBI httr IRanges RSQLite S4Vectors KEGGREST curl jsonlite mime openssl R6 bit64 blob memoise pkgconfig Rcpp plogr png Biostrings askpass bit rlang vctrs cachem XVector GenomeInfoDb crayon sys cli glue fastmap zlibbioc RCurl GenomeInfoDbData bitops org.Hs.eg.db annotate graph XML xtable 0 0.5 1 Imported methods 0 20 40 Required packages 0 2 4 Heaviness from parents Biobase hgu95a.db GSEABase In total 52 packages are required directly or indirectly (52) when installing 'GSVAdata' (1.32.0) Depends Base packages that are required Contributed packages that are required Packages that are required for installing 'GSVAdata' Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on GSVAdata
GSEABase Depends Parent package is listed in Depends of GSVAdata but no object from parent package is imported. 49 5
hgu95a.db Depends Parent package is listed in Depends of GSVAdata but no object from parent package is imported. 46 2
Biobase Depends Parent package is listed in Depends of GSVAdata but no object from parent package is imported. 5 0

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 GSVAdata Co-heaviness as Jaccard coeffcient
hgu95a.db GSEABase 39 0.848

Analysis was done with pkgndep.