Diagnostics

The daggle doctor command runs a series of health checks and reports problems.

Usage

daggle doctor

What it checks

Check	What it verifies
Tool paths	Resolved paths for Rscript, quarto, git, and sh
R version	R is installed and meets any version constraints
R platform	Reports the platform string (e.g. aarch64-apple-darwin23)
renv status	Whether renv is synchronized, out of date, or absent
Scheduler status	Whether the scheduler is running and its PID
Config paths	DAG directory, data directory, and config file locations are accessible
DAG file validity	All YAML files in the DAG directory parse without errors

Example output:

Tools:
  [OK]   rscript: /usr/local/bin/Rscript
  [OK]   quarto: /opt/homebrew/bin/quarto
  [OK]   git: /usr/bin/git
  [OK]   sh: /bin/sh

R version:       4.4.1 .............. ok
R platform:      aarch64-apple-darwin23
renv status:     synchronized ....... ok
Scheduler:       running (PID 4821).. ok
Config paths:    all accessible ..... ok
DAG files:       3 valid, 0 invalid . ok

When to run

• After installing or upgrading daggle
• When runs fail in unexpected ways
• Before filing a bug report (include the output)