IOBR Package Development Instructions

Development Environment Setup

R Installation (Using rig + pak - RECOMMENDED)

Use the modern R installation manager rig and package installer pak for optimal development experience:

# Install rig (R Installation Manager)
curl -Ls https://github.com/r-lib/rig/releases/download/latest/rig-linux-latest.tar.gz | sudo tar xz -C /usr/local

# Install latest R release
sudo rig add release

# Verify installation
rig list
R --version

Timing: rig installation ~1 minute, R installation ~5-8 minutes

Package Dependencies Installation

# Navigate to package directory
cd /path/to/IOBR

# Install all package dependencies using pak (much faster than install.packages)
R --slave -e "pak::local_install_deps()"

# Install additional development tools
R --slave -e "pak::pak(c('devtools', 'knitr', 'rmarkdown', 'testthat', 'pkgdown', 'roxygen2', 'styler', 'lintr'))"

Timing: Dependencies installation ~4-6 minutes, dev tools ~2-3 minutes

System Dependencies

Essential system packages (automatically handled by pak):

pandoc (for vignettes and documentation)
libxml2-dev, libcurl4-openssl-dev, libssl-dev (for various R packages)
Graphics libraries: libfreetype6-dev, libjpeg-dev, libpng-dev, libtiff-dev

Build and Testing Commands

Package Building

# Quick build (without vignettes) - recommended for development
R CMD build . --no-build-vignettes

# Full build (with vignettes) - for release
R CMD build .

Timing: Quick build ~10-20 seconds, Full build ~5-10 minutes

Package Checking

# Quick check (skip suggested packages)
_R_CHECK_FORCE_SUGGESTS_=false R CMD check IOBR_*.tar.gz --no-manual

# Full check (requires all suggested packages)
R CMD check IOBR_*.tar.gz --no-manual

# Using devtools (recommended)
R -e "devtools::check()"

Timing: Quick check ~2-3 minutes, Full check ~10-15 minutes

Running Tests

# Install package locally first
R --slave -e "pak::local_install('.')"

# Run tests
R --slave -e "testthat::test_dir('tests/testthat')"

# Test basic functionality
R --slave -e "library(IOBR); data('eset_stad'); print(head(eset_stad))"

Code Formatting and Quality

# Format all R code
R -e "styler::style_pkg()"

# Check code quality
R -e "lintr::lint_package()"

# Update documentation
R -e "roxygen2::roxygenise()"

Development Workflow

1. Initial Setup

cd /path/to/IOBR
R --slave -e "pak::local_install_deps()"
R --slave -e "pak::pak(c('devtools', 'roxygen2', 'styler', 'lintr'))"

2. Make Changes

Edit R files in
```
R/
```
directory
Update documentation in roxygen2 comments
Add/update tests in
```
tests/testthat/
```

3. Format and Check

# Format code
R -e "styler::style_pkg()"

# Update documentation
R -e "devtools::document()"

# Run checks
R -e "devtools::check()"

4. Test

# Install locally
R -e "devtools::install()"

# Run tests
R -e "devtools::test()"

5. Build and Verify

# Build package
R CMD build .

# Final check
R CMD check IOBR_*.tar.gz

Common Issues and Solutions

Issue: Missing dependencies

Solution: Install with pak:

R -e "pak::local_install_deps()"

Issue: Roxygen version mismatch

Solution: Update DESCRIPTION:

RoxygenNote: 7.3.3

Issue: Vignette build fails

Solution: Install knitr and rmarkdown:

R -e "pak::pak(c('knitr', 'rmarkdown'))"

Issue: Check fails with "cannot open connection"

Solution: Ensure all system dependencies are installed

Package Standards

Code Style

Use tidyverse style guide
Run
```
styler::style_pkg()
```
before committing
Maximum line length: 80 characters (documentation can exceed)

Dependencies

Minimize dependencies
Use specific packages instead of meta-packages (e.g., dplyr instead of tidyverse)
Declare all imports in DESCRIPTION
Use
```
@importFrom
```
for specific functions

Documentation

Document all exported functions with roxygen2
Include examples for all exported functions
Keep vignettes up-to-date
Run
```
devtools::document()
```
after changes

Testing

Write tests for all new functions
Aim for >80% code coverage
Run
```
devtools::test()
```
before committing

Quick Reference

# Complete check workflow
cd /path/to/IOBR
R -e "styler::style_pkg()"
R -e "devtools::document()"
R -e "devtools::check()"
R -e "devtools::test()"

# Build for distribution
R CMD build .
R CMD check IOBR_*.tar.gz --as-cran

Resources

IOBR Package Development Instructions

Development Environment Setup

R Installation (Using rig + pak - RECOMMENDED)

Use the modern R installation manager rig and package installer pak for optimal development experience:

# Install rig (R Installation Manager)
curl -Ls https://github.com/r-lib/rig/releases/download/latest/rig-linux-latest.tar.gz | sudo tar xz -C /usr/local

# Install latest R release
sudo rig add release

# Verify installation
rig list
R --version

Timing: rig installation ~1 minute, R installation ~5-8 minutes

Package Dependencies Installation

# Navigate to package directory
cd /path/to/IOBR

# Install all package dependencies using pak (much faster than install.packages)
R --slave -e "pak::local_install_deps()"

# Install additional development tools
R --slave -e "pak::pak(c('devtools', 'knitr', 'rmarkdown', 'testthat', 'pkgdown', 'roxygen2', 'styler', 'lintr'))"

Timing: Dependencies installation ~4-6 minutes, dev tools ~2-3 minutes

System Dependencies

Essential system packages (automatically handled by pak):

pandoc (for vignettes and documentation)
libxml2-dev, libcurl4-openssl-dev, libssl-dev (for various R packages)
Graphics libraries: libfreetype6-dev, libjpeg-dev, libpng-dev, libtiff-dev

Build and Testing Commands

Package Building

# Quick build (without vignettes) - recommended for development
R CMD build . --no-build-vignettes

# Full build (with vignettes) - for release
R CMD build .

Timing: Quick build ~10-20 seconds, Full build ~5-10 minutes

Package Checking

# Quick check (skip suggested packages)
_R_CHECK_FORCE_SUGGESTS_=false R CMD check IOBR_*.tar.gz --no-manual

# Full check (requires all suggested packages)
R CMD check IOBR_*.tar.gz --no-manual

# Using devtools (recommended)
R -e "devtools::check()"

Timing: Quick check ~2-3 minutes, Full check ~10-15 minutes

Running Tests

# Install package locally first
R --slave -e "pak::local_install('.')"

# Run tests
R --slave -e "testthat::test_dir('tests/testthat')"

# Test basic functionality
R --slave -e "library(IOBR); data('eset_stad'); print(head(eset_stad))"

Code Formatting and Quality

# Format all R code
R -e "styler::style_pkg()"

# Check code quality
R -e "lintr::lint_package()"

# Update documentation
R -e "roxygen2::roxygenise()"

Development Workflow

1. Initial Setup

cd /path/to/IOBR
R --slave -e "pak::local_install_deps()"
R --slave -e "pak::pak(c('devtools', 'roxygen2', 'styler', 'lintr'))"

2. Make Changes

Edit R files in
```
R/
```
directory
Update documentation in roxygen2 comments
Add/update tests in
```
tests/testthat/
```

3. Format and Check

# Format code
R -e "styler::style_pkg()"

# Update documentation
R -e "devtools::document()"

# Run checks
R -e "devtools::check()"

4. Test

# Install locally
R -e "devtools::install()"

# Run tests
R -e "devtools::test()"

5. Build and Verify

# Build package
R CMD build .

# Final check
R CMD check IOBR_*.tar.gz

Common Issues and Solutions

Issue: Missing dependencies

Solution: Install with pak:

R -e "pak::local_install_deps()"

Issue: Roxygen version mismatch

Solution: Update DESCRIPTION:

RoxygenNote: 7.3.3

Issue: Vignette build fails

Solution: Install knitr and rmarkdown:

R -e "pak::pak(c('knitr', 'rmarkdown'))"

Issue: Check fails with "cannot open connection"

Solution: Ensure all system dependencies are installed

Package Standards

Code Style

Use tidyverse style guide
Run
```
styler::style_pkg()
```
before committing
Maximum line length: 80 characters (documentation can exceed)

Dependencies

Minimize dependencies
Use specific packages instead of meta-packages (e.g., dplyr instead of tidyverse)
Declare all imports in DESCRIPTION
Use
```
@importFrom
```
for specific functions

Documentation

Document all exported functions with roxygen2
Include examples for all exported functions
Keep vignettes up-to-date
Run
```
devtools::document()
```
after changes

Testing

Write tests for all new functions
Aim for >80% code coverage
Run
```
devtools::test()
```
before committing

Quick Reference

# Complete check workflow
cd /path/to/IOBR
R -e "styler::style_pkg()"
R -e "devtools::document()"
R -e "devtools::check()"
R -e "devtools::test()"

# Build for distribution
R CMD build .
R CMD check IOBR_*.tar.gz --as-cran

IOBR Package Development Instructions

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