ggpointless
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Comparison · Infra & APIs
checkhelper vs PEIMAN2
A side-by-side editorial comparison of checkhelper and PEIMAN2 — release velocity, themes, recent moves, and the top alternatives to consider.
Shared themes:r-packages
checkhelper vs PEIMAN2: at a glance
What is checkhelper?
checkhelper grew from a check wrapper into a CRAN pre-submission auditor.
1.0.0 added a whole audit_* family — audit_downloads(), audit_description(), audit_dontrun() and audit_citation() — each parsing package source statically and returning a tibble of hits paired with a suggested fix. The package is now defending that position: 1.0.1 rc1 is a submission candidate answering a CRAN archival notice, after roxygen2 8.x moved DESCRIPTION's RoxygenNote field and broke a find_missing_tags() test fixture.
What is PEIMAN2?
PEIMAN2 cut its annotation database loose from its release cycle without breaking CRAN.
PEIMAN2 does enrichment analysis over post-translational modifications, testing whether a protein list is enriched for particular PTMs against UniProt-derived annotations, with translation functions bridging to mass spectrometry workflows. Its answers are only as current as its bundled database, and until June that database could only be refreshed by releasing a new package version. Version 1.1.0 changes that.
checkhelper vs PEIMAN2: editorial side-by-side
checkhelper
2.5INFRA · APIS
checkhelper grew from a check wrapper into a CRAN pre-submission auditor.
◆ Current state
1.0.0 added a whole audit_* family — audit_downloads(), audit_description(), audit_dontrun() and audit_citation() — each parsing package source statically and returning a tibble of hits paired with a suggested fix. The package is now defending that position: 1.0.1 rc1 is a submission candidate answering a CRAN archival notice, after roxygen2 8.x moved DESCRIPTION's RoxygenNote field and broke a find_missing_tags() test fixture.
◆ Where it's heading
The design commitment is static analysis — AST walks via getParseData(), line-by-line Rd reading, no eval() and no namespace loading — so the tool can report on a package it never runs. That commitment is what made the roxygen2 8.x break survivable: the audit pipeline itself was verified correct under 8.1.0 and only the test scaffolding had to go, now guarded by a dedicated regression test. fix_globals(write = TRUE) is being sanded down in parallel, no longer flattening per-function grouping comments or writing a degenerate empty globalVariables() shell.
◆ Prediction
The immediate move is the 1.0.1 submission itself, clearing the archival notice. Beyond that, each additional CRAN incoming-check rule remains a candidate for another audit_* function; the open question these notes still leave is whether the family ever gets a single combined entry point.
PEIMAN2
0.0INFRA · APIS
PEIMAN2 cut its annotation database loose from its release cycle without breaking CRAN.
◆ Current state
PEIMAN2 does enrichment analysis over post-translational modifications, testing whether a protein list is enriched for particular PTMs against UniProt-derived annotations, with translation functions bridging to mass spectrometry workflows. Its answers are only as current as its bundled database, and until June that database could only be refreshed by releasing a new package version. Version 1.1.0 changes that.
◆ Where it's heading
The package has been moving from a fixed snapshot toward versioned, user-selectable data. Earlier releases updated the bundled database in place — 1.0.0 shipped the March 2025 version and said little else — which meant the annotation vintage was whatever the package version implied. Now update_peiman_database() downloads and caches external database files and UniProt PTM lists, enrichment workflows take a database_version argument, and the mass-spec translators take a ptmlist_version, so an analysis can pin a dated database rather than a package release. The CRAN-safe default is preserved deliberately: loading, examples and checks still use the bundled internal data and need no network.
◆ Prediction
Version pinning is now expressible but the release notes do not describe how a chosen version is recorded in output, so surfacing the active database version in results is the natural companion. The database and the UniProt PTM list are versioned separately, which leaves room for a combined manifest.
Alternatives to checkhelper and PEIMAN2
Other Infra & APIs products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either checkhelper or PEIMAN2.
mpactr
mpactr spent two spring releases normalizing case in metadata after users kept tripping on it.
surveytidy
surveytidy taught every dplyr verb to operate on a whole collection of surveys at once.
surveycore
surveycore declared its API stable with every survey design type covered.
prospectr
prospectr spent its biggest release in years fixing spectra it had been quietly mangling.
standardlastprofile
A German electricity load-profile package added gas and doubled the market it serves.
See all checkhelper alternatives → · See all PEIMAN2 alternatives →
Recent activity from checkhelper and PEIMAN2
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1d agocheckhelpercheckhelper 1.0.1 rc1 (CRAN submission candidate)
- 2mo agoPEIMAN2Database updates decouple from package releases ⚡
- 3mo agocheckhelperA static audit_* family for CRAN pre-submission checks ⚡
- 1y agoPEIMAN2Bundled database refreshed to the March 2025 UniProt vintage
- 1y agoPEIMAN2Documentation fix for the second example dataset
- 2y agocheckhelperTest fixes for roxygen2 changes
- 2y agoPEIMAN2Background lists for SEA and PSEA; tidyverse dependency dropped
- 3y agocheckhelpercheckhelper 0.1.0 - First CRAN Release
Frequently asked questions
What is the difference between checkhelper and PEIMAN2?
Both compete on the same themes — r-packages — within Infra & APIs. checkhelper is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is checkhelper better than PEIMAN2?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. checkhelper is currently shipping more aggressively (velocity 2.5 vs 0.0), with 0 editorial sparks in the last 30 days against 0. For your specific use case, the alternatives sections above list other Infra & APIs products to evaluate alongside.
What are the best alternatives to checkhelper?
Top checkhelper alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "checkhelper alternatives" section above for the current picks, or visit /alternatives/checkhelper for the full list with editorial commentary on each.
What are the best alternatives to PEIMAN2?
Top PEIMAN2 alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "PEIMAN2 alternatives" section above for the current picks, or visit /alternatives/peiman2 for the full list with editorial commentary on each.