Finding R System Dependencies

Using pak and renv to find R system dependencies

Let’s try to get an environment of packages and understand the system dependencies. This would be useful for fresh installs into a new environment.

A note on methodology

In an ideal world a user will be able to identify what packages they are using. Do you really need that package from 3 years ago that you installed but ended up not using? Technology doesn’t solve all problems! Sometimes the “soft” method is the best way to solve a problem.

Steps

Create the current environment as a renv project and snapshot it

library(pak)
library(renv)

# Or restore a project with renv::restore() if using a pre-existing projectd
renv::init()
renv::snapshot()

Find what OS we are on

# R.version # Nope
# version # Nope
# .Platform # nope
# .Platform$OS.type # nope
# Sys.info() # nope
# Sys.info()["sysname"] # nope
# system("cat /etc/*release") # closer
# system("lsb_release -a") # closer
# pak::system_r_platform_data()$distribution # this is the one!

if(.Platform$OS.type == "unix"){
  Sys.setenv("PKG_SYSREQS_PLATFORM"=pak::system_r_platform_data()$distribution)
  print(Sys.getenv("PKG_SYSREQS_PLATFORM"))
} else { ## windows
  Sys.setenv("PKG_SYSREQS_PLATFORM"="windows") # supported by pak
  print(Sys.getenv("PKG_SYSREQS_PLATFORM"))
  warning("Windows is not support by pak")
}

Optionally, recreate the environment on another server using renv and pak

cp rserver/renv.lock /new-location 

cd /new-location && \
    echo -e 'options(renv.config.pak.enabled=TRUE)\noptions(repos=c(CRAN="https://packagemanager.posit.co/cran/__linux__/rhel9/2025-03-10")) Sys.getenv("PKG_SYSREQS_PLATFORM" > .Rprofile && \
    R -q -e 'install.packages(c("renv"))' && \
    R -q -e 'renv::activate()' && \
    R -q -e 'renv::restore()'

Find the installed packages

library(jsonlite)
library(tidyverse)
my_renvlock <- fromJSON("renv.lock")

pkgs_df<- map_dfr(my_renvlock$Packages, ~ enframe(.) |>
  filter(name %in% c("Package", "Version")) |>
  mutate(value = as.character(value)) |>
  pivot_wider())

Find the system dependencies for those installed packages

deps<-pak::pkg_sysreqs(pkgs_df$Package, upgrade = FALSE,sysreqs_platform=Sys.getenv("PKG_SYSREQS_PLATFORM"))

# Get the commands to run to install system deps to support the package environment
if (!identical(deps$pre_install,character(0))) cat(unique(deps$pre_install),sep="\n")
if (!identical(deps$install_scripts,character(0))) cat(deps$install_scripts,sep="\n")
if (!identical(deps$post_install,character(0))) cat(unique(deps$post_install),sep="\n")

Alternatively, find the most common package downloaded from package manager and support those

Credit: https://github.com/rstudio/rstudio-pro/issues/6536#issuecomment-2694317773

library(httr)
library(jsonlite)
library(pak)

base_url <- "https://packagemanager.posit.co/__api__/metrics/packages"
query_params <- list(
  "_sort" = "count",
  "_order" = "desc",
  "_days" = 30,
  "_sourceType" = "r",
  "_limit" = 1000
)

# Make the GET request
response <- GET(url = base_url, query = query_params)

if (status_code(response) == 200) {
  # Parse the JSON content
  content <- content(response, "text")
  data <- fromJSON(content)
  
  # Set platform name ()
  Sys.setenv("PKG_SYSREQS_PLATFORM"="rockylinux-9")
  # extract system reqs using pak
  deps<-pak::pkg_sysreqs(data$name)
  
  # Print commands
  if (!identical(deps$pre_install,character(0))) cat(unique(deps$pre_install),sep="\n")
  if (!identical(deps$install_scripts,character(0))) cat(deps$install_scripts,sep="\n")
  if (!identical(deps$post_install,character(0))) cat(unique(deps$post_install),sep="\n")
  
} else {
  cat("Error: Unable to fetch data from P3M. Status code:", status_code(response), "\n")
}