Audit Dependency Versions

Audit Dependency Versions

Audit deps → ver staleness, known security vulns, compat issues. Inventory all deps from lock files → check latest → classify staleness → flag security → prioritized upgrade report.

Use When

• Pre-release → deps current + secure
• Periodic maint (monthly/quarterly)
• Security advisory hits project dep
• Lang ver upgrade (R 4.4 → 4.5)
• Pre-submit CRAN/npm/crates.io
• Inheriting project → dep health

In

• Required: Project root w/ dep/lock files
• Optional: Ecosystem (R, Node.js, Python, Rust)
• Optional: Security-only mode (skip staleness → CVEs)
• Optional: Allowlist deps to skip
• Optional: Compat target date (e.g., "R 4.4.x")

Do

Step 1: Inventory All Dependencies

Parse dep files → complete inventory.

R packages:

# Direct dependencies from DESCRIPTION
grep -A 100 "^Imports:" DESCRIPTION | grep -B 100 "^[A-Z]" | head -50
grep -A 100 "^Suggests:" DESCRIPTION | grep -B 100 "^[A-Z]" | head -50

# Pinned versions from renv.lock
cat renv.lock | grep -A 3 '"Package"'

Node.js:

# Direct dependencies
cat package.json | grep -A 100 '"dependencies"' | grep -B 100 "}"
cat package.json | grep -A 100 '"devDependencies"' | grep -B 100 "}"

# Pinned versions from lock file
cat package-lock.json | grep '"version"' | head -20

Python:

# From requirements or pyproject
cat requirements.txt
cat pyproject.toml | grep -A 50 "dependencies"

# Pinned versions
cat requirements.lock 2>/dev/null || pip freeze

Rust:

# From Cargo.toml
grep -A 50 "\[dependencies\]" Cargo.toml
# Pinned versions
cat Cargo.lock | grep -A 2 "name ="

Inventory table:

| Package | Pinned Version | Type | Ecosystem |
|---|---|---|---|
| dplyr | 1.1.4 | Import | R |
| testthat | 3.2.1 | Suggests | R |
| express | 4.18.2 | dependency | Node.js |
| pytest | 8.0.0 | dev | Python |

→ Complete inventory direct + (optional) transitive deps w/ pinned vers.

If err: Lock files missing → repro issues. Note as finding → inventory from manifest w/ declared constraints.

Step 2: Check Latest Available Versions

Latest ver per dep.

R:

# Check available versions
available.packages()[c("dplyr", "testthat"), "Version"]

# Or via CLI
Rscript -e 'cat(available.packages()["dplyr", "Version"])'

Node.js:

# Check outdated packages
npm outdated --json

# Or individual package
npm view express version

Python:

# Check outdated
pip list --outdated --format=json

# Or individual
pip index versions requests 2>/dev/null

Rust:

# Check outdated
cargo outdated

# Or individual
cargo search serde --limit 1

Update inventory:

| Package | Pinned | Latest | Gap |
|---|---|---|---|
| dplyr | 1.1.4 | 1.1.6 | patch |
| ggplot2 | 3.4.0 | 3.5.1 | minor |
| Rcpp | 1.0.10 | 1.0.14 | patch |
| shiny | 1.7.4 | 1.9.1 | minor |

→ Latest ver per dep w/ gap magnitude (patch/minor/major).

If err: Registry unreachable → mark "unable to check", continue. Don't block full audit on one registry.

Step 3: Classify Staleness

Staleness level per dep:

Summary:

### Staleness Summary

- **Current**: 12 packages (48%)
- **Patch behind**: 8 packages (32%)
- **Minor behind**: 3 packages (12%)
- **Major behind**: 1 package (4%)
- **EOL/Archived**: 1 package (4%)

**Overall health**: AMBER (major-behind and EOL packages present)

Color coding:

• GREEN: All current/patch-behind
• AMBER: Any minor-behind or one major-behind
• RED: Multiple major-behind or any EOL

→ Every dep classified + overall health rating.

If err: Ver comparison ambiguous (non-SemVer, date-based) → classify conservatively "minor behind" + note non-standard scheme.

Step 4: Check for Security Vulnerabilities

Run ecosystem-specific audit tools:

R:

• No built-in audit tool; check manually
• Cross-reference with https://www.r-project.org/security.html
• Check GitHub advisories for each package

Node.js:

# Built-in audit
npm audit --json

# Severity levels: info, low, moderate, high, critical
npm audit --audit-level=moderate

Python:

# Using pip-audit
pip-audit --format=json

# Or safety
safety check --json

Rust:

# Using cargo-audit
cargo audit --json

Document findings:

### Security Findings

| Package | Version | CVE | Severity | Fixed In | Description |
|---|---|---|---|---|---|
| express | 4.18.2 | CVE-2024-XXXX | High | 4.19.0 | Path traversal in static file serving |
| lodash | 4.17.20 | CVE-2021-23337 | Critical | 4.17.21 | Command injection via template |

**Security status**: RED (1 critical, 1 high)

→ Vulns w/ CVE, severity, affected ver, fix ver.

If err: No audit tool → GitHub Security Advisories manual search per dep. Best-effort without tooling.

Step 5: Plan Upgrade Path

Prioritize by risk + impact:

### Upgrade Plan

#### Priority 1: Security Fixes (do immediately)
| Package | Current | Target | Risk | Notes |
|---|---|---|---|---|
| lodash | 4.17.20 | 4.17.21 | Low (patch) | Fixes CVE-2021-23337 |
| express | 4.18.2 | 4.19.0 | Low (minor) | Fixes CVE-2024-XXXX |

#### Priority 2: EOL Replacements (plan within 1 month)
| Package | Current | Replacement | Migration Effort |
|---|---|---|---|
| request | 2.88.2 | node-fetch 3.x | Medium (API change) |

#### Priority 3: Major Version Upgrades (plan for next release cycle)
| Package | Current | Target | Breaking Changes |
|---|---|---|---|
| webpack | 4.46.0 | 5.90.0 | Config format, plugin API |

#### Priority 4: Minor/Patch Updates (batch in maintenance window)
| Package | Current | Target | Notes |
|---|---|---|---|
| dplyr | 1.1.4 | 1.1.6 | Patch fixes only |
| ggplot2 | 3.4.0 | 3.5.1 | New geom functions added |

Major upgrades → note breaking changes from dep changelog.

→ Prioritized plan: security → EOL → major → minor/patch batches.

If err: Dep abandoned, no fork → document risk. Recommend: (1) vendor current, (2) alt pkg, (3) accept + monitor.

Step 6: Document Compatibility Risks

Per planned upgrade:

### Compatibility Assessment

#### express 4.18.2 -> 4.19.0
- **API changes**: None (patch-level fix)
- **Node.js requirement**: Same (>=14)
- **Test impact**: Run full test suite; expect zero failures
- **Confidence**: HIGH

#### webpack 4.46.0 -> 5.90.0
- **API changes**: Config file format changed, several plugins removed
- **Node.js requirement**: >=10.13 (unchanged)
- **Test impact**: Build configuration must be rewritten; all tests need re-run
- **Confidence**: LOW (requires dedicated migration effort)
- **Migration guide**: https://webpack.js.org/migrate/5/

Write report → DEPENDENCY-AUDIT.md or DEPENDENCY-AUDIT-2026-02-17.md.

→ Compat risks documented per significant upgrade. Report complete.

If err: Can't assess without testing → branch-based upgrade: branch, apply, test, evaluate, merge.

Check

• All direct deps inventoried from lock/manifest
• Latest ver checked per dep
• Staleness level assigned (current/patch/minor/major/EOL)
• Overall health rating (GREEN/AMBER/RED)
• Security audit w/ ecosystem tooling
• All CVEs documented (severity, affected, fix)
• Upgrade plan prioritized: security > EOL > major > minor/patch
• Compat risks per major upgrade
• Report → DEPENDENCY-AUDIT.md
• No "unable to check" w/o reason

Traps

• Ignore transitive deps: 10 direct → 200 transitive. Vulns hide transitive. Use npm ls / renv::dependencies().
• Upgrade all at once: Batch upgrade → can't identify regression source. Upgrade logical groups (security first, majors individually, minors/patches batched).
• "Outdated" ≠ "insecure": Major behind + no CVE < current + critical vuln. Security > freshness.
• Skip changelogs: Blind major upgrade → breaking changes in dep → breaking changes in your project.
• Audit fatigue: Audits w/o action → worthless. Policy: security → 1 sprint, EOL → 1 quarter.
• Missing lock files: No lock → non-repro builds. Finding itself critical.
• Wrong R binary on hybrid: WSL/Docker → Rscript may be cross-platform wrapper. Check which Rscript && Rscript --version. Prefer native (e.g., /usr/local/bin/Rscript). See Setting Up Your Environment.

→

• apply-semantic-versioning — ver bumps may trigger from dep upgrades
• manage-renv-dependencies — R-specific dep mgmt w/ renv
• security-audit-codebase — broader security audit inc. dep vulns
• manage-changelog — doc dep upgrades in changelog
• plan-release-cycle — schedule dep upgrades in release timeline