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scriptbuddy

scriptbuddy makes any R script or analysis folder runnable on a new machine.

It scans R code, detects required packages, follows source() files recursively, and classifies dependencies as CRAN, Bioconductor, or GitHub. It can install only what is missing, export a dependency report, and generate a reproducible renv.lock file.

This tool is designed for wet-lab scientists, collaborators, and reviewers who need R scripts to run reliably without manual package troubleshooting.

Installation

# install.packages("remotes")
remotes::install_github("dipankatanu/scriptbuddy")

How scriptbuddy works

scriptbuddy detects packages used through:

  • library() and require()
  • pkg::function() and pkg:::function()
  • pacman::p_load()
  • source() files recursively
  • GitHub installs via remotes::install_github() and devtools::install_github()

Dependencies are classified into:

  • CRAN
  • Bioconductor
  • GitHub
  • Unknown

Quick start

Scan a script without installing anything:

library(scriptbuddy)
scriptbuddy("analysis.R", install = FALSE)

Install missing packages from CRAN and Bioconductor:

scriptbuddy("analysis.R", install = TRUE)

Only missing packages are installed. Already installed packages are skipped automatically.

Copy and paste install commands

To generate explicit install commands for CRAN, Bioconductor, and GitHub:

print_install_commands("analysis.R")

Example output:

install.packages(c("dplyr", "ggplot2"))
BiocManager::install(c("limma", "edgeR"))
remotes::install_github(c("jokergoo/ComplexHeatmap"))

This is useful for sending installation instructions to collaborators.

Export a dependency report

write_deps_report("analysis.R", out_dir = "scriptbuddy_report")

This creates:

scriptbuddy_report/
├── deps.csv
├── cran.txt
├── bioc.txt
├── github.txt
└── unknown.txt

These files can be shared, archived, or attached to manuscripts.

Create a reproducible environment

scriptbuddy_lock("analysis.R", project_dir = ".")

This creates or updates a renv.lock file so the exact software environment can be reproduced on another machine.

Why scriptbuddy exists

Most R scripts fail on new machines because:

  • Required packages are missing
  • CRAN and Bioconductor repositories are confused
  • GitHub packages are forgotten
  • Dependencies are hidden inside source() files

scriptbuddy solves these problems in one command.

GitHub dependencies

GitHub packages are detected and reported, and install commands are printed for them. They are not installed automatically to avoid authentication problems, private repositories, and accidental overwrites.

License

MIT License