install-putior

name	install-putior
description	Install and configure the putior R package for workflow visualization. Covers CRAN and GitHub installation, optional dependencies (mcptools, ellmer, shiny, shinyAce, logger, plumber2), and verification of the complete annotation-to-diagram pipeline. Use when setting up putior for the first time, preparing a machine for workflow visualization tasks, when a downstream skill requires putior to be installed, or restoring an environment after an R version upgrade or renv wipe.
license	MIT
allowed-tools	Read Write Edit Bash Grep Glob
metadata	{"author":"Philipp Thoss","version":"1.0","domain":"workflow-visualization","complexity":"basic","language":"R","tags":"putior, install, workflow, mermaid, visualization, R"}

Install putior

Install the putior R package and its optional dependencies so the annotation-to-diagram pipeline is ready to use.

When to Use

• Setting up putior for the first time in a project or environment
• Preparing a machine for workflow visualization tasks
• A downstream skill (analyze-codebase-workflow, generate-workflow-diagram) requires putior to be installed
• Restoring an environment after an R version upgrade or renv wipe

Inputs

• Required: Access to an R installation (>= 4.1.0)
• Optional: Whether to install from CRAN (default) or GitHub dev version
• Optional: Which optional dependency groups to install: MCP (mcptools, ellmer), interactive (shiny, shinyAce), logging (logger), ACP (plumber2)

Procedure

Step 1: Verify R Installation

Confirm R is available and meets the minimum version requirement.

R.Version()$version.string
# Must be >= 4.1.0

# From WSL with Windows R
"/mnt/c/Program Files/R/R-4.5.2/bin/Rscript.exe" -e "cat(R.version.string)"

Expected: R version string printed, >= 4.1.0.

On failure: Install or upgrade R. On Windows, download from https://cran.r-project.org/bin/windows/base/. On Linux, use sudo apt install r-base.

Step 2: Install putior

Install from CRAN (stable) or GitHub (dev).

# CRAN (recommended)
install.packages("putior")

# GitHub dev version (if latest features needed)
remotes::install_github("pjt222/putior")

Expected: Package installs without errors. library(putior) loads silently.

On failure: If CRAN installation fails with "not available for this version of R", use the GitHub version. If GitHub fails, check that remotes is installed: install.packages("remotes").

Step 3: Install Optional Dependencies

Install optional packages based on required functionality.

# MCP server integration (for AI assistant access)
remotes::install_github("posit-dev/mcptools")
install.packages("ellmer")

# Interactive sandbox
install.packages("shiny")
install.packages("shinyAce")

# Structured logging
install.packages("logger")

# ACP server (agent-to-agent communication)
install.packages("plumber2")

Expected: Each package installs without errors.

On failure: For mcptools, ensure remotes is installed first. For system dependency errors on Linux, install the required libraries (e.g., sudo apt install libcurl4-openssl-dev for httr2 dependency).

Step 4: Verify Installation

Run the basic pipeline to confirm everything works.

library(putior)

# Check package version
packageVersion("putior")

# Verify core functions are available
stopifnot(
  is.function(put),
  is.function(put_auto),
  is.function(put_diagram),
  is.function(put_generate),
  is.function(put_merge),
  is.function(put_theme)
)

# Test basic pipeline with a temp file
tmp <- tempfile(fileext = ".R")
writeLines("# put id:'test', label:'Hello putior'", tmp)
cat(put_diagram(put(tmp)))

Expected: Mermaid flowchart code printed to console containing test and Hello putior.

On failure: If put is not found, the package did not install correctly. Reinstall with install.packages("putior", dependencies = TRUE). If the diagram is empty, verify the temp file was created and the annotation syntax uses single quotes inside double quotes.

Validation

• library(putior) loads without errors
• packageVersion("putior") returns a valid version
• put() with a file containing a valid PUT annotation returns a data frame with one row
• put_diagram() produces Mermaid code starting with flowchart
• All requested optional dependencies load without errors

Common Pitfalls

• Wrong quote nesting: PUT annotations use single quotes inside the annotation: id:'name', not id:"name" (which conflicts with the comment string delimiter in some contexts).
• Missing Pandoc for vignettes: If you plan to build putior's vignettes locally, ensure RSTUDIO_PANDOC is set in .Renviron.
• renv isolation: If the project uses renv, you must install putior inside the renv library. Run renv::install("putior") instead of install.packages("putior").
• GitHub rate limits: Installing mcptools from GitHub may fail without a GITHUB_PAT. Set one via usethis::create_github_token().

Related Skills

• analyze-codebase-workflow — next step after installation to survey a codebase
• configure-putior-mcp — set up the MCP server after installing optional deps
• manage-renv-dependencies — manage putior within an renv environment
• configure-mcp-server — general MCP server configuration