Dependency graph

library(data.table)

A dependency graph for all GitHub repos that use the rworkflows GitHub Action.

Create

Here is the code for creating the plot.

Install required packages

if(!require("echodeps"))remotes::install_github("RajLabMSSM/echodeps",
                                                dependencies = TRUE)

Create graph

res <- echodeps::dep_graph(pkg = "rworkflows",
                           method_seed = "github",
                           exclude = c("neurogenomics_rworkflows",
                                       "neurogenomics_r_workflows"),
                           #node_size = "total_downloads", 
                           reverse = TRUE,
                           save_path = here::here("reports","rworkflows_depgraph.html"))

Save data

## Save network plot as PNG
echodeps::visnet_save(res$save_path)

## Save all data and plots
saveRDS(res, here::here("reports","dep_graph_res.rds"))

Count stars/clones/views

knitr::kable(res$report)

Show

rworkflow depgraph

Hover over each node to show additional metadata.

Identify highly downloaded packages

Identify the CRAN/Bioc R packages with the most number of downloads. This guides which packages would be the most useful to focus on implementing rworkflows in.

pkgs <- echogithub::r_repos_downloads(which = c("CRAN","Bioc"))

#### Get top 10 per R repository ####
pkgs_top <- pkgs[, tail(.SD, 10), by="r_repo"] 
methods::show(pkgs_top)

Assess R repository usage

This demonstrates the need for using rworkflows, as there are 25,000 R packages that are exclusively distributes via GitHub (which may or may not have code/documentation checks).

r_repos_res <- echogithub::r_repos(save_path = here::here("reports","r_repos_upset.pdf"), width=12)

Session Info

utils::sessionInfo()

## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] data.table_1.16.4
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37     desc_1.4.3        R6_2.5.1          fastmap_1.2.0    
##  [5] xfun_0.49         cachem_1.1.0      knitr_1.49        htmltools_0.5.8.1
##  [9] rmarkdown_2.29    lifecycle_1.0.4   cli_3.6.3         sass_0.4.9       
## [13] pkgdown_2.1.1     textshaping_0.4.0 jquerylib_0.1.4   systemfonts_1.1.0
## [17] compiler_4.4.1    tools_4.4.1       ragg_1.3.2        evaluate_1.0.1   
## [21] bslib_0.8.0       yaml_2.3.10       jsonlite_1.8.9    rlang_1.1.4      
## [25] fs_1.6.5          htmlwidgets_1.6.4

Authors: Brian Schilder, Alan Murphy, Nathan Skene

Vignette updated: Dec-18-2024