实际问题
如何避免\dontrun{在包含示例的单独文件\\dontrun{中在 roxygenizing 后变成相应的 Rd 文件？
我确实找到了一种解决方法，但感觉好像我可能只是遗漏了一些明显的东西，即roxigenize().
细节
我想我注意到一个可能的错误，或者，恕我直言，在处理存储在单独文件中的roxygen2示例时（而不是在实际的 roxygen 代码中说明它），至少是一种不良行为。
问题是\dontrun{各个示例文件\\dontrun{中的行在 roxygenizing 后变成了生成的 Rd 文件。
您将在下面找到该行为的说明以及简单的解决方法
1）确保目录
dir.create("src", recursive=TRUE, showWarnings=FALSE)
dir.create("package", recursive=TRUE, showWarnings=FALSE)
# Ensure empty package directory
subdirs <- list.files("package", full.names=TRUE)
if (length(subdirs)) {
sapply(subdirs, unlink, recursive=TRUE)
}
2) 使用两种不同的嵌入示例方式创建示例函数
foo1 <- function(x) {message("I'm foo #1"); return(TRUE)}
roxy.1 <- c(
"#' Title foo1()",
"#'",
"#' Description foo1().",
"##' This line is commented out",
"#'",
"#' @param x Some R object that doesn't matter.",
"#' @return \\code{TRUE}.",
"#' @references \\url{http://www.something.com/}",
"#' @author John Doe \\email{john.doe@@something.com}",
"#' @seealso \\code{\\link{foo2}}",
"#' @example inst/examples/foo1.R"
)
ex.1 <- c(
"\\dontrun{",
"foo1()",
"}"
)
foo2 <- function(y) {message("I'm foo #2"); return(FALSE)}
roxy.2 <- c(
"#' Title foo2()",
"#'",
"#' Description foo2().",
"##' This line is commented out",
"#'",
"#' @param y Some R object that doesn't matter.",
"#' @return \\code{FALSE}.",
"#' @references \\url{http://www.something.com/}",
"#' @author John Doe \\email{john.doe@@something.com}",
"#' @seealso \\code{\\link{foo1}}",
"#' @examples",
"#' \\dontrun{",
"#' foo2()}",
"#' }"
)
write(roxy.1, file="src/foo1.R")
write(c("foo1 <-", deparse(foo1)), file="src/foo1.R", append=TRUE)
write(roxy.2, file="src/foo2.R")
write(c("foo2 <-", deparse(foo2)), file="src/foo2.R", append=TRUE)
3) 创建包骨架
package.skeleton(name="test", path="package",
code_files=c("src/foo1.R", "src/foo2.R"))
4）创建单独的示例文件foo1()
dir.create("package/test/inst/examples", recursive=TRUE, showWarnings=FALSE)
write(ex.1, file="package/test/inst/examples/foo1.R")
5) 充氧
require("roxygen2")
roxygenize(
package.dir="package/test",
overwrite=TRUE,
unlink.target=FALSE,
roclets = c("collate", "namespace", "rd")
)
6) 检查包裹
shell("R CMD check package/test", intern=FALSE)
R CMD 检查的截断输出表明\dontrun{in存在问题./package/test/man/foo1.Rd
[...]
Warning: parse error in file 'test-Ex.R':
1: unexpected input
19:
20: \
^
* checking examples ... ERROR
Running examples in 'test-Ex.R' failed
The error most likely occurred in:
> ### Name: foo1
> ### Title: Title foo1()
> ### Aliases: foo1
>
> ### ** Examples
>
> \dontrun{
Error: unexpected input in "\"
Execution halted
Warning message:
In shell(expr, intern = FALSE) :
'R CMD check package/test' execution failed with error code 1
>
7) 解决方法
patchRdFiles <- function(
path="package",
name,
...
) {
path <- file.path(path, name, "man")
if (!file.exists(path)) {
stop(paste("Invalid directory path: '", path, "'", sep=""))
}
files <- list.files(path, full.names=TRUE)
#ii=files[1]
.dead <- sapply(files, function(ii) {
cnt <- readLines(ii, warn=FALSE)
if (length(grep("\\\\\\\\dontrun", cnt, perl=TRUE))) {
message(paste("Correcting: '", ii, "'", sep=""))
write(gsub("\\\\dontrun", "\\dontrun", cnt), file=ii)
}
return(NULL)
})
return(TRUE)
}
这将删除 Rd 文件中所有重复的反斜杠：
patchRdFiles(name="test")
8) 再次检查包裹
# CHECK PACKAGE AGAIN
path <- "package/test"
expr <- paste("R CMD check", path)
shell(expr, intern=FALSE)
再次检查 R CMD 检查的截断输出。有问题的 Rd 文件现在通过了检查。当前错误是由不完整引起的./package/test/man/test-package.Rd，此时可以
[...]
Warning: parse error in file 'test-Ex.R':
11: unexpected symbol
56:
57: ~~ simple examples
^
* checking examples ... ERROR
Running examples in 'test-Ex.R' failed
The error most likely occurred in:
> ### Name: test-package
> ### Title: What the package does (short line) ~~ package title ~~
> ### Aliases: test-package test
> ### Keywords: package
>
> ### ** Examples
>
> ~~ simple examples of the most important functions ~~
Error: unexpected symbol in "~~ simple examples"
Execution halted
Warning message:
In shell(expr, intern = FALSE) :
'R CMD check package/test' execution failed with error code 1
>