Cross-Repo Dependency Audit

Check how packages in an org depend on each other and flag version mismatches. Run from ~/code/{org}/ or pass the org name as an argument. Can also run across multiple orgs (e.g. /org-deps epinowcast epiforecasts).

Helper script

A pre-built script at ~/.claude/scripts/org-deps.sh collects all dependency info in one pass. Run it first to avoid spending tokens on file parsing.

~/.claude/scripts/org-deps.sh <org-name> [org-name2 ...] > /tmp/org-deps.json

If the script is missing or not executable, flag this to the user and stop.

The script outputs a JSON array with per-repo entries containing:

repo, org, gh_org, type, version, latest_release_tag
dependencies object with R fields (depends, imports, suggests, remotes) or Julia fields (julia_deps, julia_compat)

Phase 1: Build dependency graph

From the script output, build a graph of which local packages depend on which other local packages.

Phase 2: Check for issues

Version mismatches

Package A requires primarycensored >= 1.0 but local copy is on 0.9.5
Remotes pointing to branches that no longer exist
[compat] bounds that exclude the latest release

Breaking changes

For each dependency edge, check if the upstream package has commits since the version pinned downstream that include:

Breaking changes (search NEWS.md for "breaking", "removed", "deprecated")
API changes (renamed exports, changed function signatures)

Stale pins

Downstream packages pinning old versions when newer ones are available on CRAN or in the org.

Phase 3: Report

Present:

Dependency graph (text format showing who depends on whom)
Table of issues found with severity (breaking/outdated/info)
Suggested fixes

Phase 4: Fix (with confirmation)

For each confirmed fix:

Create a worktree branch
Update version constraints
Run tests to verify compatibility
Create a PR

Auto-Exit When Standalone

IMPORTANT: If this command is being run as a standalone request, automatically exit after completing all phases successfully.