--- name: computational-environment-configuration description: Use when at the start of any DaDIA pipeline execution, or whenever you are preparing to run a complex multi-package R workflow on a new system or after updating package managers. license: CC-BY-4.0 metadata: edam_topics: [] tools: - R - XCMS - metaMS - DaDIA techniques: - LC-MS derived_from: - doi: 10.1021/acs.analchem.0c05022 title: DaDIA evidence_spans: - R Version 4.0 or above - XCMS Development Version 3.11.4 or above - metaMS Version 1.25.1 claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_dadia_cq doi: 10.1021/acs.analchem.0c05022 title: DaDIA dedup_kept_from: coll_dadia_cq schema_version: 0.2.0 attribution: generator: AgenticScienceBuilder original_doi: 10.1021/acs.analchem.0c05022 all_source_dois: - 10.1021/acs.analchem.0c05022 zenodo_doi: 10.5281/zenodo.20794027 curators: [] promoter: Louis-Félix Nothias sponsor: CNRS & Université Côte d'Azur --- # computational-environment-configuration ## Summary Validate and document software version dependencies before executing a data processing pipeline, ensuring that R, XCMS, metaMS, and all dependent packages meet minimum thresholds. This skill prevents runtime failures by establishing a reproducible computational environment contract upfront. ## When to use Apply this skill at the start of any DaDIA pipeline execution, or whenever you are preparing to run a complex multi-package R workflow on a new system or after updating package managers. Use it specifically when you have a set of DIA mzXML files ready for processing and need to guarantee that the computational environment will not fail mid-analysis due to version incompatibilities. ## When NOT to use - You are running a standalone analysis that does not depend on XCMS, metaMS, or the DaDIA pipeline. - You have already validated the environment in the current R session and have documented proof that all versions meet requirements. - Your input data are already processed feature tables or summary statistics, not raw mzXML files that require the full DaDIA dependency stack. ## Inputs - Current R installation (queried at runtime) - Installed XCMS package (if present) - Installed metaMS package (if present) - System package repository state ## Outputs - Structured validation report (JSON or text) with per-dependency version check status - Overall pipeline-ready boolean flag - Pass/fail status for R version check - Pass/fail status for XCMS version check - Pass/fail status for metaMS version check ## How to apply Execute a structured four-step validation workflow: (1) Query the installed R version using version$major and version$minor; reject pipeline execution if the major version is below 4. (2) Load the XCMS package, extract its version string, and compare against the minimum requirement (≥3.11.4) using semantic versioning rules; fail if below threshold. (3) Load the metaMS package and extract its version string; verify exact or compatible match to version 1.25.1 and flag any mismatch. (4) Generate a structured validation report (JSON or text format) that summarizes all three version checks with individual pass/fail status for each dependency and an overall pipeline-ready boolean flag. The rationale is that mismatched versions can silently alter algorithm behavior or cause load-time errors; documenting this contract ensures transparency and reproducibility. ## Related tools - **R** (Runtime environment and version query engine; minimum version 4.0 required) - **XCMS** (Mass spectrometry data processing package; minimum development version 3.11.4 required) - **metaMS** (Metabolomics data analysis package; exact version 1.25.1 required) - **DaDIA** (Data-dependent acquisition pipeline that orchestrates XCMS and metaMS; subject to validated environment) — github.com/HuanLab/DaDIA ## Evaluation signals - All three version checks (R, XCMS, metaMS) complete without errors or exceptions. - The overall pipeline-ready flag is true; if false, the specific failing dependency is clearly identified. - The validation report is machine-readable (JSON or structured text) and can be version-controlled or logged for audit. - Subsequent DaDIA pipeline execution succeeds without version-related warnings or silent algorithmic changes. - The number of samples declared in line 38 of the DaDIA configuration matches the count of real DIA mzXML files in the input directory. ## Limitations - This skill only validates declared version thresholds; it does not detect transitive dependency conflicts or missing optional packages. - Exact version matching for metaMS (1.25.1) may be overly strict if newer patch versions are backward-compatible; compatibility rules are not documented. - The skill does not validate R library paths, disk space, memory availability, or other environmental factors that could cause runtime failure. - If all other packages are updated to newest available versions as recommended, there is no explicit check that these newer versions remain compatible with the specified XCMS and metaMS versions. ## Evidence - [readme] R Version 4.0 or above, XCMS Development Version 3.11.4 or above, and metaMS Version 1.25.1 are required; all other packages should be updated to the newest available version.: "R Version 4.0 or above, XCMS Development Version 3.11.4 or above, and metaMS Version 1.25.1 are required; all other packages should be updated to the newest available version." - [other] Query the installed R version using version$major and version$minor; verify that the major version is ≥4 and reject execution 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." - [other] Load the XCMS package and extract its version string; parse and compare against the minimum requirement (≥3.11.4) using semantic versioning rules; fail if below threshold.: "Load the XCMS package and extract its version string; parse and compare against the minimum requirement (≥3.11.4) using semantic versioning rules; fail if below threshold." - [other] 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.: "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] The number of samples in line 38 has to agree with the real number of DIA mzXML files: "The number of samples in line 38 has to agree with the real number of DIA mzXML files"