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- Qualify base and package calls in R/ with pkg:: (stats, utils, grDevices, graphics, shiny, ggplot2, grid, ComplexHeatmap, ...) - Column names in aes()/dplyr verbs via the .data pronoun - importFrom for %>%, R6Class and .data; globalVariables for the session objects the bind_to_scope() helpers read - devtools from Imports to Suggests; dendextend and rlang to Imports - .Rbuildignore CITATION.cff and SKILLS.md Assisted-by: AI coding agent
@description and @PARAM for every public method of ExploreDataset, ExploreDatasetSE, ExploreDatasetH5AD and ExploreDatasetParquet, so devtools::document() runs without roxygen warnings. man/ regenerated with roxygen2 8.1.1. Assisted-by: AI coding agent
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Cleans up what
make checkreports, apart from one NOTE that needs a decision (below).Result
main(564572b)make documentChanges
R6 method docs (commit 2):
@description/@paramfor every public method ofExploreDataset,ExploreDatasetSE,ExploreDatasetH5AD,ExploreDatasetParquetman/regenerated with roxygen2 8.1.1NOTE "R code for possible problems" (commit 1):
R/qualified withpkg::(stats::setNames,ggplot2::aes,grid::gpar,dendextend::colored_bars, …), the styleR/already uses elsewhereaes()and dplyr verbs via.data$importFromfor%>%,R6Class,.datautils::globalVariables()foreds,input,seqAnnoReactive: the session objects thebind_to_scope()helpers read (Keep one copy of the 6 session-bound helpers, in R/ (part of #10) #12)NOTEs "top-level files" and "CITATION file in a non-standard place":
CITATION.cffandSKILLS.mdadded to.RbuildignoreDESCRIPTION:
devtoolsfrom Imports to Suggests: nothing in the package or app uses itdendextendandrlangfrom Suggests to Imports: the package code now calls themProd: no base-image change;
dendextendandrlangare already attached byapp.R.Not fixed: "Namespaces in Imports field not imported from"
24 packages (
DT,plotly,shinydashboard,tidyverse, …) are used only byinst/app/, which R CMD check does not scan;rhdf5is needed by anndataR to read.h5ad. They have to stay in Imports. Options: keep the NOTE, or reference them once from an internal function so check sees them.Verification
make check(macOS, R 4.6.2): 0 errors, 0 warnings; tests passair format . --check: cleanR/, as on prod), demo dataset: Summary, Ordination (samples plot, biplot), Heatmaps, Boxplots, Replicability (heatmap, dendrogram, dendrogram PDF download); no errors in the R logmain: 3 tests intest-prolfquapp_h5ad.Rfail underdevtools::test()but pass in R CMD checkPrepared with the assistance of an AI coding agent.