Dependency analysis on package globaltest

General information

Bioconductor link link
Package version5.50.0
Number of strong dependencies53
Number of all dependencies96
Number of parent packages6
Max heaviness from parent packages5
Total heaviness from parent packages8
Number of parent packages (including Suggests and Enhances)21
Max co-heaviness from parent packages ("annotate" and "AnnotationDbi")38

Dependency heatmap

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

Adjust heatmap size:
Base packages Other packages Depends Imports Suggests stats graphics methods utils grDevices stats4 tools grid splines BiocGenerics Biobase rlang R6 crayon zlibbioc IRanges S4Vectors pkgconfig Rcpp httr png Biostrings vctrs curl jsonlite mime openssl XVector GenomeInfoDb cli glue askpass RCurl GenomeInfoDbData sys bitops DBI RSQLite KEGGREST bit64 blob memoise plogr bit cachem fastmap AnnotationDbi Matrix lattice XML xtable graph survival RColorBrewer viridisLite RcppArmadillo data.table affy limma ggplot2 affyio BiocManager preprocessCore digest gtable isoband MASS mgcv scales tibble withr nlme farver labeling lifecycle munsell ellipsis fansi magrittr pillar colorspace utf8 org.Hs.eg.db annotate 0 5 10 Imported methods 0 20 40 Required packages 0 10 20 Heaviness from parents methods survival graphics Biobase AnnotationDbi annotate gss boot rpart MASS golubEsets lungExpression Rgraphviz penalized mstate KEGGREST GO.db org.Hs.eg.db vsn hu6800.db GSEABase In total 53 packages are required directly or indirectly (96) when installing 'globaltest' (5.50.0) Depends Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'globaltest' Imported functions The whole namespace is imported


Dependency table

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

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

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on globaltest
survival Depends 6 0 0 9 5
methods Depends The whole set of functions/methods/classes from parent package is imported to the namespace of globaltest. 0 0
annotate Imports 1 0 0 47 3
graphics Imports 13 0 0 0 0
Biobase Imports The whole set of functions/methods/classes from parent package is imported to the namespace of globaltest. 5 0
AnnotationDbi Imports 6 0 0 44 0
vsn Suggests No object is imported into the namespace of globaltest. 46 28
mstate Suggests No object is imported into the namespace of globaltest. 14 4
Rgraphviz Suggests No object is imported into the namespace of globaltest. 9 2
penalized Suggests No object is imported into the namespace of globaltest. 12 2
hu6800.db Suggests No object is imported into the namespace of globaltest. 46 2
GSEABase Suggests No object is imported into the namespace of globaltest. 49 2
gss Suggests No object is imported into the namespace of globaltest. 1 1
boot Suggests No object is imported into the namespace of globaltest. 2 1
rpart Suggests No object is imported into the namespace of globaltest. 3 1
MASS Suggests No object is imported into the namespace of globaltest. 5 1
golubEsets Suggests No object is imported into the namespace of globaltest. 6 1
lungExpression Suggests No object is imported into the namespace of globaltest. 6 1
GO.db Suggests No object is imported into the namespace of globaltest. 45 1
org.Hs.eg.db Suggests No object is imported into the namespace of globaltest. 45 1
KEGGREST Suggests No object is imported into the namespace of globaltest. 27 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 globaltest Co-heaviness as Jaccard coeffcient
AnnotationDbi annotate 38 0.927

Analysis was done with pkgndep.