The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

Dependency graph


Authors: Brian Schilder, Alan Murphy, Nathan Skene


Vignette updated: Jan-18-2024

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 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Sonoma 14.2.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## time zone: Europe/London
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] data.table_1.14.10 rworkflows_1.0.1  
## 
## loaded via a namespace (and not attached):
##  [1] gtable_0.3.4        jsonlite_1.8.8      renv_1.0.3         
##  [4] dplyr_1.1.4         compiler_4.3.1      BiocManager_1.30.22
##  [7] tidyselect_1.2.0    jquerylib_0.1.4     rvcheck_0.2.1      
## [10] scales_1.3.0        yaml_2.3.8          fastmap_1.1.1      
## [13] here_1.0.1          ggplot2_3.4.4       R6_2.5.1           
## [16] generics_0.1.3      knitr_1.45          yulab.utils_0.1.2  
## [19] tibble_3.2.1        desc_1.4.3          dlstats_0.1.7      
## [22] rprojroot_2.0.4     munsell_0.5.0       bslib_0.6.1        
## [25] pillar_1.9.0        RColorBrewer_1.1-3  rlang_1.1.2        
## [28] utf8_1.2.4          cachem_1.0.8        badger_0.2.3       
## [31] xfun_0.41           fs_1.6.3            sass_0.4.8         
## [34] memoise_2.0.1.9000  cli_3.6.2           magrittr_2.0.3     
## [37] digest_0.6.33       grid_4.3.1          lifecycle_1.0.4    
## [40] vctrs_0.6.5         evaluate_0.23       glue_1.6.2         
## [43] fansi_1.0.6         colorspace_2.1-0    rmarkdown_2.25     
## [46] tools_4.3.1         pkgconfig_2.0.3     htmltools_0.5.7

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.