library(data.table)
A dependency graph for all GitHub repos that use the rworkflows
GitHub Action.
Here is the code for creating the plot.
if(!require("echodeps"))remotes::install_github("RajLabMSSM/echodeps",
dependencies = TRUE)
res <- echodeps::dep_graph(pkg = "rworkflows",
method_seed = "github",
exclude = c("neurogenomics_rworkflows",
"neurogenomics_r_workflows"),
node_size = "total_downloads",
height="100%",
reverse = TRUE,
save_path = here::here("reports","rworkflows_depgraph.html"))
saveRDS(res, here::here("reports","dep_graph_res.rds"))
knitr::kable(res$report)
Hover over each node to show additional metadata.
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)
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)
utils::sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur ... 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
##
## locale:
## [1] C/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] data.table_1.14.8 rworkflows_0.99.13 BiocStyle_2.26.0
##
## loaded via a namespace (and not attached):
## [1] bslib_0.4.2 compiler_4.2.1 pillar_1.9.0
## [4] RColorBrewer_1.1-3 BiocManager_1.30.20 jquerylib_0.1.4
## [7] yulab.utils_0.0.6 tools_4.2.1 digest_0.6.31
## [10] jsonlite_1.8.4 evaluate_0.21 lifecycle_1.0.3
## [13] tibble_3.2.1 gtable_0.3.3 pkgconfig_2.0.3
## [16] rlang_1.1.1 cli_3.6.1 rvcheck_0.2.1
## [19] yaml_2.3.7 xfun_0.40 fastmap_1.1.1
## [22] dplyr_1.1.2 knitr_1.44 desc_1.4.2
## [25] generics_0.1.3 sass_0.4.6 vctrs_0.6.3
## [28] dlstats_0.1.7 rprojroot_2.0.3 grid_4.2.1
## [31] tidyselect_1.2.0 here_1.0.1 glue_1.6.2
## [34] R6_2.5.1 fansi_1.0.4 rmarkdown_2.22
## [37] bookdown_0.34 ggplot2_3.4.2 badger_0.2.3
## [40] magrittr_2.0.3 scales_1.2.1 htmltools_0.5.5
## [43] colorspace_2.1-0 renv_0.17.3 utf8_1.2.3
## [46] munsell_0.5.0 cachem_1.0.8