我有一个R使用roxygen2. 它有一些C代码/src，我刚刚开始使用Doxygen. 有什么方法可以结合文档或将编译与 roxygen2 集成？C将代码文档放在哪里的任何“最佳实践” ？
谷歌搜索 roxygen2 和 doxygen 主要导致roxygen 类似于 doxygen结果。我发现了一些带有 Doxyfiles 的包，但没有一致的组织。例如，lme4输出到源目录之外的inst/doc/Doxyfile一个文件夹。在 Matrix 的根目录下还有一个 Doxyfile（但在以前的版本中是在.doxygenlme4inst
是否有任何理由不将C文档包含在包中，或者为什么 Doxygen 很少在 R 包中使用，尽管广泛使用C?
更新：查看相关的 roxygen2 功能请求
我个人在我在所有脚本中调用的“dataManagement”包中使用以下代码。它有 roxygen 文档和示例。实际上，您只需调用 document() 并在 src/ 中的 C 代码上运行 doxygen。该文档放在 inst/doxygen 中，以便您的包准备好 CRAN。
R 文档是为不应该查看 C 代码的 R最终用户设计的.
library("testthat")
library("devtools")
#' @title Replace a value for a given tag on file in memory
#' @description Scan the lines and change the value for the named tag if one line has this tag,
#' add a line at the end if no line has this tag and return a warning if several lines
#' matching the tag
#' @param fileStrings A vector with each string containing a line of the file
#' @param tag The tag to be searched for
#' @param newVal The new value for the tag
#' @return The vector of strings with the new value
#' @examples
#' fakeFileStrings <- c("Hello = world","SURE\t= indeed","Hello = you")
#'
#' expect_warning(ReplaceTag(fakeFileStrings,"Hello","me"))
#'
#' newFake <- ReplaceTag(fakeFileStrings,"SURE","me")
#' expect_equal(length(newFake), length(fakeFileStrings))
#' expect_equal(length(grep("SURE",newFake)), 1)
#' expect_equal(length(grep("me",newFake)), 1)
#'
#' newFake <- ReplaceTag(fakeFileStrings,"Bouh","frightened?")
#' expect_equal(length(newFake), length(fakeFileStrings)+1)
#' expect_equal(length(grep("Bouh",newFake)), 1)
#' expect_equal(length(grep("frightened?",newFake)), 1)
ReplaceTag <- function(fileStrings,tag,newVal){
iLine <- grep(paste0("^",tag,"\\>"),fileStrings)
nLines <- length(iLine)
if(nLines == 0){
line <- paste0(tag,"\t= ",newVal)
iLine <- length(fileStrings)+1
}else if (nLines > 0){
line <- gsub("=.*",paste0("= ",newVal),fileStrings[iLine])
if(nLines >1){
warning(paste0("File has",nLines,"for key",tag,"check it up manually"))
}
}
fileStrings[iLine] <- line
return(fileStrings)
}
#' Prepares the R package structure for use with doxygen
#' @description Makes a configuration file in inst/doxygen
#' and set a few options:
#' \itemize{
#' \item{EXTRACT_ALL = YES}
#' \item{INPUT = src/}
#' \item{OUTPUT_DIRECTORY = inst/doxygen/}
#' }
#' @param rootFolder The root of the R package
#' @return NULL
#' @examples
#' \dontrun{
#' DoxInit()
#' }
#' @export
DoxInit <- function(rootFolder="."){
doxyFileName <- "Doxyfile"
initFolder <- getwd()
if(rootFolder != "."){
setwd(rootFolder)
}
rootFileYes <- length(grep("DESCRIPTION",dir()))>0
# prepare the doxygen folder
doxDir <- "inst/doxygen"
if(!file.exists(doxDir)){
dir.create(doxDir,recursive=TRUE)
}
setwd(doxDir)
# prepare the doxygen configuration file
system(paste0("doxygen -g ",doxyFileName))
doxyfile <- readLines("Doxyfile")
doxyfile <- ReplaceTag(doxyfile,"EXTRACT_ALL","YES")
doxyfile <- ReplaceTag(doxyfile,"INPUT","src/")
doxyfile <- ReplaceTag(doxyfile,"OUTPUT_DIRECTORY","inst/doxygen/")
cat(doxyfile,file=doxyFileName,sep="\n")
setwd(initFolder)
return(NULL)
}
#' devtools document function when using doxygen
#' @description Overwrites devtools::document() to include the treatment of
#' doxygen documentation in src/
#' @param doxygen A boolean: should doxygen be ran on documents in src?
#' the default is TRUE if a src folder exist and FALSE if not
#' @return The value returned by devtools::document()
#' @example
#' \dontrun{
#' document()
#' }
#' @export
document <- function(doxygen=file.exists("src")){
if(doxygen){
doxyFileName<-"inst/doxygen/Doxyfile"
if(!file.exists(doxyFileName)){
DoxInit()
}
system(paste("doxygen",doxyFileName))
}
devtools::document()
}