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Export only the documented API (removes the Rd warning) - #7
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exploreDE(), build_explore_h5ad(), new_explore_dataset(), validate_explore_dataset() and the ExploreDataset* R6 classes stay exported. The other 89 objects get @nord instead of @export: the app sources R/ in production and, since #5, attaches the namespace when installed; tests run in the namespace. This removes the 19 Rd files with 63 undocumented arguments (R CMD check WARNING).
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Stacked on #6: merge #6 first; GitHub then retargets this PR to
main.Of 99 exports, only 4 functions are documented for users (README, vignette, AI skill, h5ad spec). The other 95 were exported so the installed app could see them; since #5 the installed app attaches the package namespace, so that is no longer needed. The 19 Rd files with 63 undocumented arguments (the remaining R CMD check WARNING) all belong to those app helpers.
Exported after this PR (11)
exploreDE(),build_explore_h5ad(),new_explore_dataset(),validate_explore_dataset()ExploreDataset,ExploreDatasetH5AD,ExploreDatasetSE,ExploreDatasetSE_CountQC,ExploreDatasetSE_CrisprCountQC,ExploreDatasetSE_Proteomics,ExploreDatasetSE_RNASeq(their Rd pages document the methods users call onnew_explore_dataset()results)Commits
eaf8598:@export→@noRdfor the 89 other objects (88 exported helpers plusse_from_prolfquapp_anndata, which was tagged but never exported); NEWS bullet under Breaking changes02f0aad:make documentoutput: NAMESPACE (99 → 11 exports), 88 Rd files removed,man/is_prolfquapp_anndata.Rdadded (its block has@keywords internal),man/build_explore_h5ad.Rdcaught up,RoxygenNote7.3.3Why nothing breaks
R/into the app; exports are irrelevant theretest_check()runs them inside the namespace; the 5 existingexploreDE:::calls keep workingexploreDE::calls to the helpers anywhere in the ShinyProxy apps or the prolfqua packagesChecked locally
R CMD check(macOS, with vignettes): 0 WARNINGs; Rd usage, cross-references, missing documentation, code/doc mismatches, examples and vignette all OK. The one ERROR is the 3prolfquapp_h5adtests, which skip on CI (prolfquapp not installed there).exploreDE::exploreDE(): 11 exports, page loads (HTTP 200), internal helpers visible, no errors.Prepared with the assistance of an AI coding agent.