Rmarkdown不将系统命令的结果输出到html文件 [英] Rmarkdown not outputting results of system command to html file

问题描述

我是Markdown的新手，并且在SO上寻找与此类似的问题，但没有成功.我正在使用Rmarkdown(与Rstudio和knitr一起)编写一个小插图，该小插图描述了作为包的一部分导入的数据文件中的读取.我可以使用

I'm new to using Markdown, and have looked for a similar problem to this on SO without success. I'm using Rmarkdown (with Rstudio and knitr) to write a vignette that describes reading in a datafile which is imported as part of the package. I can correctly access the datafile using

> system.file("extdata", "Marlin-tag38606.txt", package = "xtractomatic")

我想在小插图中显示此文件的前几行，因此我的代码为

I want to show the first few lines of this file in the vignette, so my code reads

```{r, results=as.is}

datafile <- system.file("extdata", "Marlin-tag38606.txt", package = "xtractomatic")

system(paste("head -n5 ",datafile))

```

问题是此调用的结果输出到Rmarkdown控制台，而不输出到小插图html文件.

The problem is that the results of this call are output to the Rmarkdown console and NOT to the vignette html file.

RStudio的Rmarkdown窗口中的输出为(但格式更好):

The output in the Rmarkdown window of RStudio is (but formatted nicer):

 |...................                                              |  29%
label: unnamed-chunk-8
date    lon lat lowLon  higLon  lowLat  higLat
4/23/2003   203.899 19.664  203.899 203.899 19.664  19.664
4/24/2003   204.151 19.821  203.912597  204.389403  18.78051934 20.86148066
4/30/2003   203.919 20.351  203.6793669 204.1586331 18.79728188 21.90471812
5/1/2003    204.229 20.305  203.9943343 204.4636657 18.90440013 21.70559987
  |....................                                             |  31%

这是我想要输出到小插图文本的内容，但是它不存在.在生成的小插图中，我所拥有的只是R代码的两行，而不是系统调用的输出. 任何意见，将不胜感激.谢谢.

Which is what I wanted outputted to the vignette text, but it is not there. Within the resulting vignette all I have is the two lines of R code, but not the output from the system call. Any advice would be appreciated. Thanks.

卡拉·威尔逊

推荐答案

将intern = TRUE用于system()，然后将cat()用作输出:

Use intern = TRUE for system(), then cat() the output:

cat(system(paste("head -n5", datafile), intern = TRUE), sep = '\n')

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