How do I install the Security Audit R Package skill?

Run npx skillmds@latest add waldronlab/security-audit-r-package in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

What does the Security Audit R Package skill do?

Perform comprehensive security audit of R/Bioconductor packages It is listed under Security on SkillMD.

Is Security Audit R Package safe to use?

This skill has not completed SkillMD's automated safety review yet. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Security Audit R Package?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Security Audit R Package free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Security Audit R Package?

waldronlab (@waldronlab) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Security Audit R Package by waldronlab

Name: Security Audit R Package
Author: waldronlab

File contents

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

Determine Audit Scope: Default is the entire package (DESCRIPTION, NAMESPACE, R/, src/). The user may specify a subset.
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.
Read Files: Read all files within the defined scope.
Analyze for Issues: Review the code against the checklist defined in the gist. Address vulnerabilities, native code safety, code quality, and dependency risks.
Generate Report: Produce a structured markdown report including findings with the required fields (Issue Type Label, Severity, Location, Description, Fix).
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:

Confirms scope: DESCRIPTION, NAMESPACE, R/, src/
Fetches gist instructions and reads files.
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.

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

---name: security-audit-r-packagedescription: Perform comprehensive security audit of R/Bioconductor packages---# security-audit-r-packagePerform comprehensive security audits of R/Bioconductor packages, identifying vulnerabilities, native code security issues, code quality problems, and dependency risks.## UsageInvoke 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.## Process1. **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 FormatGenerate 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.```markdown# 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.---**Reference**: Security audit criteria defined at https://gist.github.com/lwaldron/0606c678e7d81b012a1b05901cf4b732

Frequently asked questions

Security Audit R Package