我做了一个小包装来重现该问题：
# example package
devtools::install_github("privefl/minipkg")
# example Rmd
rmd <- system.file("extdata", "Matrix.Rmd", package = "minipkg")
writeLines(readLines(rmd)) ## see content
# works fine
rmarkdown::render(
rmd,
"all",
envir = new.env(),
encoding = "UTF-8"
)
# !! does not work !!
minipkg::my_render(rmd)
minipkg::my_render ## see source code
我不明白为什么行为不同以及如何解决此问题。
编辑：我知道我可以使用Matrix::t()。我的问题更多是“为什么在这种特殊情况下而不是在所有其他情况下（例如rmarkdown::render()在包外部调用），为什么需要使用它？”。
Quitting from lines 10-13 (Matrix.Rmd)
Error in t.default(mat) : argument is not a matrix
---
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(Matrix)
mat <- rsparsematrix(10, 10, 0.1)
t(mat)
```
> # example package
> devtools::install_github("privefl/minipkg")
Downloading GitHub repo privefl/minipkg@master
? checking for file ‘/private/var/folders/md/03gdc4c14z18kbqwpfh4jdfc0000gr/T/RtmpKefs4h/remotes685793b9df4/privefl-minipkg-c02ae62/DESCRIPTION’ ...
? preparing ‘minipkg’:
? checking DESCRIPTION meta-information ...
? checking for LF line-endings in source and make files and shell scripts
? checking for empty or unneeded directories
? building ‘minipkg_0.1.0.tar.gz’
* installing *source* package ‘minipkg’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (minipkg)
> # example Rmd
> rmd <- system.file("extdata", "Matrix.Rmd", package = "minipkg")
> writeLines(readLines(rmd)) ## see content
---
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(Matrix)
mat <- rsparsematrix(10, 10, 0.1)
t(mat)
```
> # works fine
> rmarkdown::render(
+ rmd,
+ "all",
+ envir = new.env(),
+ encoding = "UTF-8"
+ )
processing file: Matrix.Rmd
|............. | 20%
ordinary text without R code
|.......................... | 40%
label: setup (with options)
List of 1
$ include: logi FALSE
|....................................... | 60%
ordinary text without R code
|.................................................... | 80%
label: unnamed-chunk-1
|.................................................................| 100%
ordinary text without R code
output file: Matrix.knit.md
/usr/local/bin/pandoc +RTS -K512m -RTS Matrix.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output Matrix.html --email-obfuscation none --self-contained --standalone --section-divs --template /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /var/folders/md/03gdc4c14z18kbqwpfh4jdfc0000gr/T//RtmpKefs4h/rmarkdown-str68525040df1.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --metadata pagetitle=Matrix.utf8.md
Output created: Matrix.html
> # !! does not work !!
> minipkg::my_render(rmd)
processing file: Matrix.Rmd
|............. | 20%
ordinary text without R code
|.......................... | 40%
label: setup (with options)
List of 1
$ include: logi FALSE
|....................................... | 60%
ordinary text without R code
|.................................................... | 80%
label: unnamed-chunk-1
Quitting from lines 10-13 (Matrix.Rmd)
Error in t.default(mat) : argument is not a matrix
> minipkg::my_render ## see source code
function (rmd)
{
rmarkdown::render(rmd, "all", envir = new.env(), encoding = "UTF-8")
}
<bytecode: 0x7f89c416c2a8>
<environment: namespace:minipkg>
>
问题是envir = new.env()。你需要的是envir = new.env(parent = globalenv())：
devtools::install_github("privefl/minipkg")
rmd <- system.file("extdata", "Matrix.Rmd", package = "minipkg")
minipkg::my_render(rmd)
# Fails
f <- minipkg::my_render
body(f) <- quote(rmarkdown::render(rmd, "all", envir = new.env(parent = globalenv()), encoding = "UTF-8"))
ns <- getNamespace("minipkg")
unlockBinding("my_render", ns)
assign("my_render", f, envir = ns)
minipkg::my_render(rmd)
# Patched one works :)
查看 的默认参数，new.env()发现默认的父环境是parent.frame()。请注意，从控制台来看，这将是globalenv()，而在包内，这将是此包命名空间（与包环境不同！）。
您可以使用 获取包命名空间getNamespace("pkg")。它是包含包的所有（也是内部）对象的环境。问题在于，这个环境在某种意义上与 R 中通常的搜索/方法查找机制“断开”，因此即使它们附加到search().
现在选择new.env(parent = globalenv())将父环境设置为搜索路径的顶部，从而能够找到所有附加的方法。
这三种方法都会生成正确的 html 文件：
#' Render an Rmd file
#' @param rmd Path of the R Markdown file to render.
#' @export
my_render <- function(rmd) {
rmarkdown::render(
rmd,
"all",
envir = new.env(parent = globalenv()),
encoding = "UTF-8"
)
}
#' Render an Rmd file
#' @param rmd Path of the R Markdown file to render.
#' @export
my_render2 <- function(rmd) {
cl <- parallel::makePSOCKcluster(1)
on.exit(parallel::stopCluster(cl), add = TRUE)
parallel::clusterExport(cl, "rmd", envir = environment())
parallel::clusterEvalQ(cl, {
rmarkdown::render(rmd, "all", encoding = "UTF-8")
})[[1]]
}
#' Render an Rmd file
#' @param rmd Path of the R Markdown file to render.
#' @export
my_render3 <- function(rmd) {
system2(
command = "R",
args = c("-e", shQuote(sprintf("rmarkdown::render('%s', 'all', encoding = 'UTF-8')", gsub("\\\\", "/", normalizePath(rmd))))),
wait = TRUE
)
}
现在比较它们的速度很有趣：
> microbenchmark::microbenchmark(my_render("inst/extdata/Matrix.Rmd"), my_render2("inst/extdata/Matrix.Rmd"), my_render3("inst/extdata/Matrix.Rmd"), times = 10L)
[...]
Unit: milliseconds
expr min lq mean median uq max neval
my_render("inst/extdata/Matrix.Rmd") 352.7927 410.604 656.5211 460.0608 560.3386 1836.452 10
my_render2("inst/extdata/Matrix.Rmd") 1981.8844 2015.541 2163.1875 2118.0030 2307.2812 2407.027 10
my_render3("inst/extdata/Matrix.Rmd") 2061.7076 2079.574 2152.0351 2138.9546 2181.1284 2377.623 10
envir = new.env(globalenv())是迄今为止最快的（几乎比替代方案快 4 倍）system2。