Dependency analysis on package geneplotter

General information

Bioconductor link link
Package version1.74.0
Number of strong dependencies51
Number of all dependencies58
Number of parent packages12
Max heaviness from parent packages3
Total heaviness from parent packages5
Number of parent packages (including Suggests and Enhances)17
Max co-heaviness from parent packages ("AnnotationDbi" and "annotate")38

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests utils graphics stats methods grDevices stats4 tools grid BiocGenerics Biobase 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 AnnotationDbi XML xtable org.Hs.eg.db graph 0 5 10 15 Imported methods 0 20 40 Required packages 0 1 2 3 Heaviness from parents methods BiocGenerics Biobase lattice annotate graphics grDevices grid RColorBrewer stats utils AnnotationDbi fibroEset Rgraphviz hgu95av2.db hu6800.db hgu133a.db In total 51 packages are required directly or indirectly (58) when installing 'geneplotter' (1.74.0) Depends Imports Suggests Base packages that are required Contributed packages that are required Packages that are required for installing 'geneplotter' Imported functions Imported S4 methods Imported S4 classes Package is listed in 'Imports' but namespace is not imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on geneplotter
annotate Depends 2 6 0 47 3
lattice Depends Parent package is listed in Depends of geneplotter but no object from parent package is imported. 5 1
methods Depends 0 0 5 0 0
BiocGenerics Depends 0 1 0 4 0
Biobase Depends 2 5 1 5 0
RColorBrewer Imports 1 0 0 0 1
graphics Imports 16 0 0 0 0
grDevices Imports 7 0 0 0 0
grid Imports 6 0 0 0 0
stats Imports 8 0 0 0 0
utils Imports 1 0 0 0 0
AnnotationDbi Imports 0 7 0 44 0
Rgraphviz Suggests No object is imported into the namespace of geneplotter. 9 2
hgu95av2.db Suggests No object is imported into the namespace of geneplotter. 46 2
hu6800.db Suggests No object is imported into the namespace of geneplotter. 46 2
hgu133a.db Suggests No object is imported into the namespace of geneplotter. 46 2
fibroEset Suggests No object is imported into the namespace of geneplotter. 6 1

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 geneplotter Co-heaviness as Jaccard coeffcient
annotate AnnotationDbi 38 0.927

Analysis was done with pkgndep.