rpkgs

Prints to stdout unique packages used in R scripts.

Description

A cli tool that scan R files and extract the packages used.

It parses packages from these methods:

• library(pkg) / require(pkg)
• pkg::func()
• pacman::p_load(pkg1, pkg2, ...) (or multi-line calls)

Include options to print additional information:

• Filename where each package is used.
• Package version or empty if package is not installed.
• Package dependencies.
• Package recursive dependencies.
• Version for dependencies or recursive dependencies.

Dependencies work only for packages available at CRAN and needs internet connection.

Usage

usage: rpkgs [-dHrv] file1 ...

Scan R files for packages used.

Options:
  -H  print with filename
  -d  dependencies
  -r  recursive dependencies (implies -d)
  -v  package version

Install

After configure SU in Makefile:

make install

Uninstall

make remove

Examples

List packages found in file:

$ rpkgs test_files/00_test.R 
ENMeval
geodata
terra
predicts
usdm

Scan multiple files and add filenames, similar to grep -H:

rpkgs -H test_files/00_test.R test_files/01_test.R
test_files/00_test.R:ENMeval
test_files/00_test.R:geodata
test_files/00_test.R:terra
test_files/00_test.R:predicts
test_files/00_test.R:usdm
test_files/01_test.R:randomForest
test_files/01_test.R:terra
test_files/01_test.R:geodata
test_files/01_test.R:usdm

Show packages and their version:

$ rpkgs -v test_files/00_test.R
ENMeval:2.0.5.2
geodata:0.6.9
terra:1.9.34
predicts:0.2.2
usdm:2.1.7

The same but with dependencies. For ease of reading, pipe into column(1):

$ rpkgs -dv 00_test.R | column -t -s ":"
ENMeval   2.0.5.2  methods             4.6.1
ENMeval   2.0.5.2  terra               1.9.34
ENMeval   2.0.5.2  maxnet              0.1.4
ENMeval   2.0.5.2  predicts            0.2.2
ENMeval   2.0.5.2  parallel            4.6.1
ENMeval   2.0.5.2  foreach             1.5.2
ENMeval   2.0.5.2  utils               4.6.1
ENMeval   2.0.5.2  stats               4.6.1
ENMeval   2.0.5.2  grDevices           4.6.1
ENMeval   2.0.5.2  dplyr               1.2.1
ENMeval   2.0.5.2  tidyr               1.3.2
ENMeval   2.0.5.2  ggplot2             4.0.3
ENMeval   2.0.5.2  glmnet              5.0
ENMeval   2.0.5.2  rangeModelMetadata  0.1.5
ENMeval   2.0.5.2  rlang               1.3.0
geodata   0.6.9    terra               1.9.34
geodata   0.6.9    rappdirs            0.3.4
terra     1.9.34   methods             4.6.1
terra     1.9.34   Rcpp                1.1.2
predicts  0.2.2    methods             4.6.1
predicts  0.2.2    terra               1.9.34
usdm      2.1.7    methods             4.6.1
usdm      2.1.7    terra               1.9.34
usdm      2.1.7    raster              3.6.32

Find which packages need to be installed by checking that version is empty with awk(1):

$ rpkgs -v 03_test.R | awk -F ":" '$2=="" { print $1 }'
multcomp
metafor
patchwork
ggpubr
gridGraphics
here
ggthemes
vcd
statpsych
pacman

Bugs

• At the moment, does not work for Rmd and qmd files.
• Fails to parse correctly when a package is loaded inside a function.