Pipeline Prerequisite Checking

pipeline-prerequisite-checking

Summary

Validate software dependencies and version requirements before executing a scientific pipeline, ensuring all critical tools meet minimum thresholds to prevent runtime failures. This skill reconstructs environment prerequisites through systematic version extraction, semantic comparison, and structured reporting.

When to use

Before launching the DaDIA metabolomics pipeline or any multi-package workflow, when you have an R environment with potentially mixed or unknown package versions and need to confirm that R ≥4.0, XCMS ≥3.11.4, metaMS ≥1.25.1, and all other dependencies are current before processing DIA mzXML files.

When NOT to use

• When the pipeline has already begun executing (prerequisite checks must run before workflow starts, not mid-execution).
• If you only need to check R version in isolation without verifying dependent packages; use lightweight version checks instead.
• When working with a pre-validated or containerized environment (Docker/Conda lock file) where versions are already guaranteed.

Inputs

• R installation with loaded package metadata (version object, XCMS package, metaMS package)
• System environment or .libPaths() pointing to installed R packages

Outputs

• Structured validation report (JSON or text) with per-package version status
• Overall pipeline-ready boolean flag (TRUE/FALSE)
• Pass/fail status for R, XCMS, and metaMS individual checks
• Execution allow/reject decision

How to apply

Execute four sequential checks in the R environment: (1) query the installed R version using version$major and version$minor, verifying major version ≥4 and rejecting execution if not met; (2) load the XCMS package, extract its version string, and parse it using semantic versioning rules to confirm ≥3.11.4; (3) load metaMS, extract its version string, and verify exact or compatible match to version 1.25.1, flagging any mismatch; (4) confirm all other packages are updated to the newest available version. Generate a structured validation report (JSON or text format) that summarizes all version checks with pass/fail status for each dependency and returns an overall pipeline-ready boolean flag. Reject pipeline execution if any critical dependency fails its threshold check.

Related tools

• R (Environment runtime and version control system; must be ≥4.0 for DaDIA compatibility)
• XCMS (Metabolomics data processing package; development version 3.11.4 or above required for DaDIA peak detection and alignment)
• metaMS (Mass spectrometry metabolite annotation package; version 1.25.1 required for DaDIA compound identification)
• DaDIA (Parent pipeline that depends on prerequisite checking before execution) — https://github.com/HuanLab/DaDIA

Evaluation signals

• R major version integer extracted and compared to threshold ≥4; execution halted if major < 4.
• XCMS version string parsed and semantic version tuple (major, minor, patch) computed; confirmed ≥3.11.4 before proceeding.
• metaMS version string extracted and matched to version 1.25.1; any mismatch flagged in report.
• All three checks aggregated into boolean pipeline-ready flag; flag = TRUE only if all three pass their thresholds.
• Validation report is generated and contains explicit pass/fail status for each of R, XCMS, metaMS, and overall readiness decision.

Limitations

• The skill validates only the three named critical dependencies (R, XCMS, metaMS) and does not exhaustively check all transitive dependencies or system-level prerequisites (e.g., C libraries, compiler versions).
• metaMS version is checked for exact or compatible match to 1.25.1; minor version drift in other packages may introduce subtle runtime incompatibilities not caught by this check.
• The skill assumes all packages are already installed in the R library path; it does not handle package installation or download failures.

Evidence

• [readme] R Version 4.0 or above, XCMS Development Version 3.11.4 or above, and metaMS Version 1.25.1 are required: "R Version 4.0 or above, XCMS Development Version 3.11.4 or above, and metaMS Version 1.25.1 are required"
• [intro] Query R version using version$major and version$minor; verify major ≥4 and reject if not: "Query the installed R version using version$major and version$minor; verify that the major version is ≥4 and reject execution if not"
• [intro] Load XCMS, extract version string, parse and compare against ≥3.11.4 using semantic versioning: "Load the XCMS package and extract its version string; parse and compare against the minimum requirement (≥3.11.4) using semantic versioning rules"
• [intro] Generate structured validation report with pass/fail status and overall pipeline-ready flag: "Generate a structured validation report (JSON or text format) summarizing all three version checks with pass/fail status for each dependency and an overall pipeline-ready boolean flag"
• [readme] Number of samples must agree with real number of DIA mzXML files in input configuration: "The number of samples in line 38 has to agree with the real number of DIA mzXML files"