## ----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], knitr = citation("knitr")[1], RefManageR = citation("RefManageR")[1], rmarkdown = citation("rmarkdown")[1], sessioninfo = citation("sessioninfo")[1], testthat = citation("testthat")[1], iSEEhub = citation("iSEEhub")[1] ) ## ----"install", eval = FALSE------------------------------------------------------------------------------------------ # if (!requireNamespace("BiocManager", quietly = TRUE)) { # install.packages("BiocManager") # } # # BiocManager::install("iSEEhub") # # ## Check that you have a valid Bioconductor installation # BiocManager::valid() ## ----"citation"------------------------------------------------------------------------------------------------------- ## Citation info citation("iSEEhub") ## ----"start", message=FALSE------------------------------------------------------------------------------------------- library(iSEEhub) library(ExperimentHub) ehub <- ExperimentHub() app <- iSEEhub(ehub) if (interactive()) { shiny::runApp(app, port = 1234) } ## ----createVignette, eval=FALSE--------------------------------------------------------------------------------------- # ## Create the vignette # library("rmarkdown") # system.time(render("iSEEhub.Rmd", "BiocStyle::html_document")) # # ## Extract the R code # library("knitr") # knit("iSEEhub.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"))