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.

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Installation

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

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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

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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.

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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.

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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.

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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.

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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.

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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.

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License

MIT License