## ----setup, include = FALSE------------------------------------------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE-------------------------------------------------------- ## Track time spent on making the vignette startTime <- Sys.time() ## Bib setup library("RefManageR") ## Write bibliography information bib <- c( R = citation(), BiocStyle = citation("BiocStyle")[1], biocthis = citation("biocthis")[1], covr = citation("covr")[1], devtools = citation("devtools")[1], fs = citation("fs")[1], glue = citation("glue")[1], knitr = citation("knitr")[1], pkgdown = citation("pkgdown")[1], rlang = citation("rlang")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], sessioninfo = citation("sessioninfo")[1], styler = citation("styler")[1], testthat = citation("testthat")[1], usethis = citation("usethis")[1] ) ## ----bioccheck_example, eval = FALSE---------------------------------------------------------------------------------- # ## Use the following for the latest options # BiocCheck::usage() # ## Disable formatting checks # BiocCheck::BiocCheck(`--no-check-formatting` = TRUE) ## ----createVignette, eval=FALSE--------------------------------------------------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("biocthis_dev_notes.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("biocthis_dev_notes.Rmd", tangle = TRUE) ## ----reproduce1, echo=FALSE------------------------------------------------------------------------------------------- ## Date the vignette was generated Sys.time() ## ----reproduce2, echo=FALSE------------------------------------------------------------------------------------------- ## Processing time in seconds totalTime <- diff(c(startTime, Sys.time())) round(totalTime, digits = 3) ## ----reproduce3, echo=FALSE------------------------------------------------------------------------------------------- ## Session info library("sessioninfo") options(width = 120) session_info() ## ----vignetteBiblio, results = 'asis', echo = FALSE, warning = FALSE, message = FALSE--------------------------------- ## Print bibliography PrintBibliography(bib, .opts = list(hyperlink = "to.doc", style = "html"))