Check all is OK

Is everything in place before your R course?

Author

Søren O’Neill

Published

January 10, 2024

1 Check your R installation

Assuming you now have a working installation of R and RStudio, do the following:

Show me how to

1. First unfold the call-out box below (‘Installation checker’)

2. Next copy the code presented in the code listing by clicking the clip-board icon in the right hand corner of the code listing filed, which appears on mouse-over

3. Close the call-out box again

Installation checker

# This script is intented to test whether the basic
# requirements for an R-installation is met, prior
# to taking part in the R4PHD courses.

### Operating system

sys_name <- Sys.info()[['sysname']]
sys_version <- Sys.info()[['release']]
sys_machine <- Sys.info()[['machine']]

if (sys_name %in% c("Linux", "MacOS", "Windows")) {
  print(paste0("[OK] Your operating system is ", sys_name, " (version ", sys_version,")"))
} else {
  print(paste0("[WARNING] Your operating system is reported as '", sys_name, "'. 'Linux', MacOS' or 'Windows' was expected."))
}

### CPU architecture

if (sys_machine %in% c("x86_64", "amd64", "arm64", "x86-64")) {
  print("[OK] You computer has a 64 bit CPU")
} else if (sys_machine %in% c("i386", "i586", "i686")) {
  print("[WARNING] You computer has an older 32 bit CPU")
} else {
  print(paste0("[WARNING] You computer is reported as ",sys_machine," ... not what was expected."))
}

### R version

r_version_major <- R.Version()[['major']]
r_version_string <- R.Version()[['version.string']]

if (r_version_major >= "4") {
  print(paste0("[OK] R installation is: ", r_version_string))
} else {
  print(paste0("[WARNING] An R version 4.x.x is recommended. You installation is ", r_version_string))
}

### RStudio version

rstudio_type <- rstudioapi::versionInfo()$mode
rstudio_version <- rstudioapi::versionInfo()$version

if (rstudio_type == "desktop") {
  print("[OK] The RStudio installation is 'desktop'")
} else {
  print(paste0("[WARNING] The RStudio installation is '", rstudio_type,"'. Version 'desktop' is recommended!"))
}

if (rstudio_version > "2023") {
  print(paste0("[OK] The RStudio version is ",rstudio_version))
} else {
  print(paste0("[WARNING] The RStudio version is ",rstudio_version, ". Version 2023+ was expected."))
}

all_installed_packages <- .packages(all.available = TRUE)
recommended_packages <- c("tidyverse", "here", "skimr", "gt", "gtExtras", "gtsummary", "patchwork", "naniar", "reprex", "ggstatsplot", "easystats", "vroom")

for (p in recommended_packages) {
  if (p %in% all_installed_packages) {
    print(paste0("[OK] '", p, "' (package) is installed."))
  } else {
    print(paste0("[WARNING] '", p, "' (package) is NOT installed."))
  }
}

4. Open RStudio

5. Create a new, empty R Script by keyboard: CTRL-SHIFT-n or menu: File / New File / R Script

6. Paste the code into the empty document

7. Execute all the code by keyboard: CTRL-SHIFT-s, or menu: Code / Source or mouse: click ‘Source’ in the top-right hand corner of the text editor panel.

8. Examine the output in the Console