这个问题是我尝试通过knitr和rmarkdown R软件包从R Markdown文档创建可重现报告的一些经验的必然结果.虽然看起来像.Rmd => HTML转换是从RStudio(Knit HTML按钮)中自动完成的,我尝试在RStudio(Rscript -e’库(rmarkdown)之外做同样的事情; render(“knitr-example-slides-1.Rmd”)’)失败到期根据消息,我的系统缺乏pandoc.这很可能是错误的,因为RStudio以某种方式设法执行转换.因此,它很可能是访问和/或路径问题.

如果不知道RStudio维护pandoc的位置和访问细节,我决定自己安装pandoc.不幸的是,sudo apt-get install pandoc并不是很有帮助,因为Ubuntu可靠存储库(14.04LTS)中当前版本的pandoc是1.12.2.1.根据rmarkdown的消息,需要1.12.3或更高版本. “没什么大不了的”,我想,并且在存储库(http://johnmacfarlane.net/pandoc/installing.html)中版本太旧的情况下遵循安装pandoc的说明.这需要安装Haskell平台,这个平台非常大,输出相当冗长.过了一段时间,我终于遇到了以下失败消息：

[ 6 of 57] Compiling Text.Pandoc.Readers.TeXMath ( src/Text/Pandoc/Readers/TeXMath.hs,dist/build/Text/Pandoc/Readers/TeXMath.o )

src/Text/Pandoc/Readers/TeXMath.hs:30:38:
    Ambiguous occurrence `readTeXMath'
    It could refer to either `Text.Pandoc.Readers.TeXMath.readTeXMath',defined at src/Text/Pandoc/Readers/TeXMath.hs:56:1
                          or `Text.TeXMath.readTeXMath',imported from `Text.TeXMath' at src/Text/Pandoc/Readers/TeXMath.hs:33:1-19
                             (and originally defined in `Text.TeXMath.Parser')
Failed to install pandoc-1.12.4.2
cabal: Error: some packages Failed to install:
pandoc-1.12.4.2 Failed during the building phase. The exception was:
ExitFailure 1
pandoc-citeproc-0.3.1 depends on pandoc-1.12.4.2 which Failed to install.

首先,我不确定如何解决它.其次,我非常怀疑应该有一种更简单的方法来享受使用rmarkdown和pandoc生成可重现的报告.您的建议将不胜感激！

更新(见评论)：

Rscript -e 'library(rmarkdown); render("knitr-example-slides-1.Rmd")'


processing file: knitr-example-slides-1.Rmd
  |.......                                                          |  11%
  ordinary text without R code

  |..............                                                   |  22%
label: setup (with options)
List of 1
 $include: logi FALSE

Quitting from lines 6-8 (knitr-example-slides-1.Rmd)
Error in eval(expr,envir,enclos) : object 'opts_chunk' not found
Calls: render ... handle -> withCallingHandlers -> withVisible -> eval -> eval

Execution halted