Dependency analysis on package RCy3

General information

Bioconductor link link
Package version2.16.0
Number of strong dependencies46
Number of all dependencies67
Number of parent packages18
Max heaviness from parent packages8
Total heaviness from parent packages22
Number of parent packages (including Suggests and Enhances)23
Max co-heaviness from parent packages ("IRkernel" and "IRdisplay")15

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of RCy3 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 RCy3.

Adjust heatmap size:
Base packages Other packages Imports Suggests methods utils stats grDevices tools graphics stats4 grid jsonlite glue digest htmltools base64enc rlang fastmap evaluate R6 repr crayon pillar cli ellipsis fansi lifecycle utf8 vctrs backports bitops BiocGenerics curl mime openssl askpass sys IRdisplay pbdZMQ uuid magrittr yaml xfun highr stringr stringi knitr jquerylib tinytex bslib sass fs rappdirs Matrix pkgconfig lattice bookdown rmarkdown BiocManager 0 2 4 6 Imported methods 0 10 20 30 Required packages 0 5 10 15 Heaviness from parents methods utils stats uuid uchardet base64enc RColorBrewer RJSONIO fs glue base64url XML RCurl BiocGenerics graph httr IRdisplay IRkernel grDevices igraph knitr rmarkdown BiocStyle In total 46 packages are required directly or indirectly (67) when installing 'RCy3' (2.16.0) Imports Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'RCy3' Imported functions The whole namespace is imported


Dependency table

"Import" information is from the NAMESPACE file of RCy3.

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 RCy3: number of required packages that can be reduced if moving parent package to Suggests of RCy3.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on RCy3
httr Imports 6 0 0 9 8
IRkernel Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RCy3. 23 3
base64url Imports 1 0 0 1 2
RCurl Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RCy3. 2 2
graph Imports 6 0 0 6 2
uchardet Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RCy3. 0 1
RColorBrewer Imports 1 0 0 0 1
RJSONIO Imports 3 0 0 1 1
fs Imports 1 0 0 1 1
XML Imports 3 0 0 2 1
methods Imports 2 0 0 0 0
utils Imports 5 0 0 0 0
stats Imports 2 0 0 0 0
uuid Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RCy3. 0 0
base64enc Imports The whole set of functions/methods/classes from parent package is imported to the namespace of RCy3. 0 0
glue Imports 1 0 0 1 0
BiocGenerics Imports 4 0 0 4 0
IRdisplay Imports 4 0 0 19 0
BiocStyle Suggests No object is imported into the namespace of RCy3. 30 16
rmarkdown Suggests No object is imported into the namespace of RCy3. 27 13
knitr Suggests No object is imported into the namespace of RCy3. 12 7
igraph Suggests No object is imported into the namespace of RCy3. 10 6
grDevices Suggests No object is imported into the namespace of RCy3. 0 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 RCy3 Co-heaviness as Jaccard coeffcient
IRdisplay IRkernel 15 0.833

Analysis was done with pkgndep.