Prepare package for Bioconductor submission#6
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- DESCRIPTION: Rewrite Title/Description, add biocViews, URL, BugReports, VignetteBuilder, bump R >= 4.4.0, add BiocStyle/knitr/rmarkdown to Suggests - Add BiocStyle vignette (vignettes/ribiosExpression.Rmd) - Convert NEWS to NEWS.md - Add @return tags to all exported generics and functions - Fix typos (annotaiton, suing, coereced, DesignContras, feta.name) - Replace class(x) %in% with is.numeric() - Replace 1:length()/1:ncol()/1:nlevels() with seq_len()/seq_along() - Replace subset()/with() with direct $ indexing in truncateDgeTable - Remove internal Roche wiki URL from documentation - Update http to https for Broad Institute URLs - Fix positional argument in writeGct eSet method - Remove duplicate @exportMethod on setter generics - Add @Format and @examples to data documentation - Update .Rbuildignore
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Documentation
@returntags to all exported generics and functions@formatand@examplesto data documentation@paramtext into@detailssections@exportMethodon setter genericsCode quality (BiocCheck compliance)
class(x) %in%withis.numeric()1:length()/1:ncol()/1:nlevels()withseq_len()/seq_along()subset()/with()with direct$indexingwriteGcteSet methodNew files
vignettes/ribiosExpression.Rmd)NEWS.md(converted from freeform NEWS)Cleanup
.RbuildignoreRemaining items before submission
Remotesfield from DESCRIPTIONroxygen2::roxygenise()R CMD checkandBiocCheck