## ----vignetteSetup, echo=FALSE, message=FALSE, warning = FALSE-----------
## Track time spent on making the vignette
startTime <- 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'),
    derfinderH = citation('derfinderHelper')[1], 
    knitrBootstrap = citation('knitrBootstrap'), 
    knitr = citation('knitr')[3],
    rmarkdown = citation('rmarkdown')),
    file = 'derfinderHelperRef.bib')
bib <- read.bibtex('derfinderHelperRef.bib')

## Assign short names
names(bib) <- c('knitcitations', 'derfinderHelper', 'knitrBootstrap',
    'knitr', 'rmarkdown')


## ----createVignette, eval=FALSE, bootstrap.show.code=FALSE---------------
## ## Create the vignette
## library('knitrBootstrap')
## 
## knitrBootstrapFlag <- packageVersion('knitrBootstrap') < '1.0.0'
## if(knitrBootstrapFlag) {
##     ## CRAN version
##     library('knitrBootstrap')
##     system.time(knit_bootstrap('derfinderHelper.Rmd', chooser=c('boot',
##         'code'), show_code = TRUE))
##     unlink('derfinderHelper.md')
## } else {
##     ## GitHub version
##     library('rmarkdown')
##     system.time(render('derfinderHelper.Rmd',
##         'knitrBootstrap::bootstrap_document'))
## }
## ## Note: if you prefer the knitr version use:
## # library('rmarkdown')
## # system.time(render('derfinder.Rmd', 'html_document'))
## 
## ## Extract the R code
## library('knitr')
## knit('derfinderHelper.Rmd', tangle = TRUE)


## ----reproducibility1, echo=FALSE, bootstrap.show.code=FALSE-------------
## Date the vignette was generated
Sys.time()


## ----reproducibility2, echo=FALSE, bootstrap.show.code=FALSE-------------
## Processing time in seconds
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits=3)


## ----reproducibility3, echo=FALSE, bootstrap.show.code=FALSE, bootstrap.show.message=FALSE----
## Session info
library('devtools')
session_info()


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