## ----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] ) ## ----"install", eval = FALSE-------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("biocthis") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----'install_dev', eval = FALSE---------------------------------------------- # BiocManager::install("lcolladotor/biocthis") ## ----"citation"--------------------------------------------------------------- ## Citation info citation("biocthis") ## ----"start", message=FALSE--------------------------------------------------- library("biocthis") ## Load other R packages used in this vignette library("usethis") library("styler") ## ----'create_example_pkg'----------------------------------------------------- ## Create an example package for illustrative purposes. ## Note: you do not need to run this for your own package! pkgdir <- biocthis_example_pkg("biocthispkg", use_git = TRUE) ## ----'create_dev'------------------------------------------------------------- ## Create the bioc templates biocthis::use_bioc_pkg_templates() ## ----'style_code'------------------------------------------------------------- ## Automatically style the example package styler::style_pkg(pkgdir, transformers = biocthis::bioc_style()) ## ----'bioc_citation'---------------------------------------------------------- ## Create a template CITATION file that is Bioconductor-friendly biocthis::use_bioc_citation() ## ----'bioc_description'------------------------------------------------------- ## Create a template DESCRIPTION file that is Bioconductor-friendly biocthis::use_bioc_description() ## ----'bioc_github_action'----------------------------------------------------- ## Create a GitHub Actions workflow that is Bioconductor-friendly biocthis::use_bioc_github_action() ## ----"biocthis_options"------------------------------------------------------- ## Open your .Rprofile file with usethis::edit_r_profile() ## For biocthis options("biocthis.pkgdown" = TRUE) options("biocthis.testthat" = TRUE) ## ----'bioc_issue'------------------------------------------------------------- ## Create a template GitHub issue file that is Bioconductor-friendly biocthis::use_bioc_issue_template() ## ----'bioc_news'-------------------------------------------------------------- ## Create a template NEWS.md file that is Bioconductor-friendly biocthis::use_bioc_news_md() ## ----'bioc_readme_rmd'-------------------------------------------------------- ## Create a template README.Rmd file that is Bioconductor-friendly biocthis::use_bioc_readme_rmd() ## ----'bioc_support'----------------------------------------------------------- ## Create a template GitHub support file that is Bioconductor-friendly biocthis::use_bioc_support() ## ----'bioc_vignette'---------------------------------------------------------- ## Create a template vignette file that is Bioconductor-friendly biocthis::use_bioc_vignette("biocthispkg", "Introduction to biocthispkg") ## ----createVignette, eval=FALSE----------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("biocthis.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("biocthis.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"))