R/createMakefile.R

In rebook: Re-using Content in Bioconductor Books

#' Create a compilation Makefile
#'
#' Create a Makefile for compiling individual chapters, 
#' in a manner that respects the dependencies between chapters.
#'
#' @inheritParams buildChapterGraph
#' @param fname String containing the name of the output Makefile.
#' @param ... Further arguments to pass to \code{\link{buildChapterGraph}}.
#'
#' @return A Makefile is created in \code{dir} with the name \code{fname}
#' and a \code{NULL} is invisibly returned.
#'
#' @details
#' The main benefit of using a Makefile is that the generation of the chapter caches can be done in parallel.
#' Then, the \pkg{bookdown} step can just serially retrieve the cache contents for rapid rendering. 
#' 
#' The Makefile uses the markdown output file as an indicator of successful \code{\link{knit}}ting of a chapter.
#' Caches are left in the current working directory after the compilation of each report.
#' It is assumed that \pkg{bookdown}'s \code{render_book} is smart enough to find and use these caches.
#'
#' @seealso
#' \code{\link{buildChapterGraph}}, to detect dependencies between chapters.
#' 
#' @examples
#' dir <- tempfile()
#' dir.create(dir)
#'
#' tmp1 <- file.path(dir, "alpha.Rmd")
#' write(file=tmp1, "```{r, echo=FALSE, results='asis'}
#' rebook::chapterPreamble()
#' ```
#' 
#' ```{r}
#' rodan <- 1
#' ```")
#'
#' tmp2 <- file.path(dir, "bravo.Rmd")
#' write(file=tmp2, "```{r, echo=FALSE, results='asis'}
#' rebook::chapterPreamble()
#' ```
#' 
#' ```{r}
#' extractCached('alpha.Rmd')
#' ```")
#' 
#' # Creating the Makefile:
#' createMakefile(dir)
#' cat(readLines(file.path(dir, "Makefile")), sep="\n")
#' 
#' @author Aaron Lun
#' @export
createMakefile <- function(dir=".", pattern="\\.Rmd$", ..., fname="Makefile") {
    g <- buildChapterGraph(dir, pattern=pattern, ...) 
    reports <- names(igraph::topo_sort(g))

    path <- file.path(dir, fname)
    to.md <- sub(pattern, ".md", reports)
    write(file=path, paste(c("all:", to.md), collapse=" "))

    for (v in seq_along(reports)) {
        parents <- names(igraph::neighbors(g, reports[v], mode="in"))

        write(sprintf("\n%s: %s\n\tR -e \"knitr::knit('%s')\"", 
            to.md[v], 
            paste(c(reports[v], to.md[match(parents, reports)]), collapse=" "),
            reports[v]),
            file=path, append=TRUE)
    }

    invisible(NULL)
}