security-audit-r-package

name	security-audit-r-package
description	Perform comprehensive security audit of R/Bioconductor packages
version	1.0.0
category	r-packages
tags	["security","bioconductor","quality-control","validation","audit"]
author	waldronlab

security-audit-r-package

Perform comprehensive security audits of R/Bioconductor packages, identifying vulnerabilities, native code security issues, code quality problems, and dependency risks.

Usage

Invoke this skill to audit an R package:

• "Run security audit on this R package"
• "Check this package for security vulnerabilities"
• "Security audit only the R/ directory"

Prerequisites

• Working directory is an R package.
• Internet access to fetch audit instructions from the reference gist.

Process

1. Determine Audit Scope: Default is the entire package (DESCRIPTION, NAMESPACE, R/, src/). The user may specify a subset.
2. Fetch Audit Instructions: Read the standardized security audit instructions from: https://gist.github.com/lwaldron/0606c678e7d81b012a1b05901cf4b732 These instructions define the categories to check, standardized issue type labels, and required fields.
3. Read Files: Read all files within the defined scope.
4. Analyze for Issues: Review the code against the checklist defined in the gist. Address vulnerabilities, native code safety, code quality, and dependency risks.
5. Generate Report: Produce a structured markdown report including findings with the required fields (Issue Type Label, Severity, Location, Description, Fix).
6. Output Report: Display the report and confirm completion.

Output Format

Generate a security report tailored to the context (full package vs quick check). All reports must include:

• Standardized labels from the gist.
• Severity levels (Critical, High, Medium, Low).
• Clear indications if no issues are found.

# Security Audit Report: [Package Name]

**Scope**: [audited files/directories]

## Summary
[Brief summary of findings]

## Findings
### [Issue Title]
**Issue Type**: [Label]
**Severity**: [Level]
**Location**: [file:line]
**Description**: [Details]
**Fix**: [Recommendation]

Examples

Example: Full Package Audit

User: "Run security audit on this R package" Agent:

1. Confirms scope: DESCRIPTION, NAMESPACE, R/, src/
2. Fetches gist instructions and reads files.
3. Analyzes for vulnerabilities and generates report. Output: A detailed report listing any High/Medium/Low issues, or a Clean status if no issues are found.

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Reference: Security audit criteria defined at https://gist.github.com/lwaldron/0606c678e7d81b012a1b05901cf4b732