## ----vignetteSetup, echo = FALSE, message = FALSE, warning = FALSE-------
## Track time spent on making the vignette
startTimeVignette <- Sys.time()

## Bib setup
library('knitcitations')

## Load knitcitations with a clean bibliography
cleanbib()
cite_options(hyperlink = 'to.doc', citation_format = 'text', style = 'html')
# Note links won't show for now due to the following issue
# https://github.com/cboettig/knitcitations/issues/63

## Write bibliography information
write.bibtex(c(knitcitations = citation('knitcitations'), 
    derfinder = citation('derfinder')[1], 
    regionReport = citation('regionReport')[1],
    knitrBootstrap = citation('knitrBootstrap'),
    ggbio = citation('ggbio'),
    ggplot2 = citation('ggplot2'),
    knitr = citation('knitr')[3],
    rmarkdown = citation('rmarkdown')),
    file = 'derfinderPlotRef.bib')
bib <- read.bibtex('derfinderPlotRef.bib')

## Assign short names
names(bib) <- c('knitcitations', 'derfinder', 'regionReport', 'knitrBootstrap',
    'ggbio', 'ggplot2', 'knitr', 'rmarkdown')


## ----createVignette, eval=FALSE, bootstrap.show.code=TRUE----------------
## ## Create the vignette
## library('knitrBootstrap')
## 
## knitrBootstrapFlag <- packageVersion('knitrBootstrap') < '1.0.0'
## if(knitrBootstrapFlag) {
##     ## CRAN version
##     system.time(knit_bootstrap('regionReport.Rmd', chooser=c('boot', 'code'), show_code = TRUE))
##     unlink('regionReport.md')
## } else {
##     ## GitHub version
##     library('rmarkdown')
##     system.time(render('regionReport.Rmd',
##         'knitrBootstrap::bootstrap_document'))
## }
## ## Note: if you prefer the knitr version use:
## # library('rmarkdown')
## # system.time(render('regionReport.Rmd', 'html_document'))
## 
## ## Extract the R code
## library('knitr')
## knit('regionReport.Rmd', tangle = TRUE)
## 
## ## Copy report output to be distributed with the package for comparison
## ## purposes
## file.copy(file.path('report', 'html', 'basicExploration.html'),
##     '../inst/basicExploration/basicExploration.html', overwrite=TRUE)
## 
## ## Clean up
## file.remove('derfinderPlotRef.bib')
## #unlink('regionReport_files', recursive=TRUE)
## unlink('report', recursive = TRUE)


## ----vignetteReproducibility1, echo=FALSE--------------------------------
## Date the report was generated
Sys.time()


## ----vignetteReproducibility2, echo=FALSE, bootstrap.show.code=FALSE-----
## Processing time in seconds
totalTimeVignette <- diff(c(startTimeVignette, Sys.time()))
round(totalTimeVignette, digits=3)


## ----vignetteReproducibility3, echo=FALSE--------------------------------
## Session info
library('devtools')
session_info()


## ----vignetteBiblio, results='asis', echo=FALSE--------------------------
## Print bibliography
bibliography()