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Report generation actions

  • Difficulty level: easy
  • Time need to lean: 10 minutes or less
  • Key points:
    • Action report generates plain text output and can be used to produce arbitrary log messages.
    • Action pandoc processes input document with pandoc
    • Action Rmarkdown process input document with Rmarkdown

Action report

Action report writes some content to an output stream. The input can either be a string or content of one or more files specified by option input. The output is determined by parameter output.

  • If output='filename', the content will be written to a file.
  • If output=obj and obj has a write function (e.g. a file handle), the content will be passed to the write function
  • If output is unspecified, the content will be written to standard output.

For example, the content of report actions is printed to standard output if no output is specified.

In [1]:
Runing 10

Runing 20

We can specify an output file with option output, but the output will be overwritten if multiple actions write to the same file

In [2]:
Runing 20

Action report can also take the content of one or more input files and write them to the output stream, after the script content (if specified). For example, the report action in the following example writes the content of out.txt to the default report stream (which is the standard output in this case).

In [3]:
Summary Report:

* result from step 10

* result from step 20

Action pandoc

Action pandoc uses command pandoc to convert specified input to output. This input to this action can be specified from option script (usually specified in script format) and input.

First, if a script is specified, pandoc assumes it is in markdown format and convert it by default to 'HTML' format. For example,

In [4]:
<h1 id="this-is-header">this is header</h1>
<p>This is some test, with <strong>emphasis</strong>.</p>

You can specify an output with option output

In [5]:

You can convert input file to another file type using a different file extension

In [6]:

Or you can add more options to the command line by modifying args,

In [7]:
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'tmp9c9k9jhr'

The second usage of the pandoc action is to specify one or more input filenames. You have to use the function form of this action as follows

In [8]:

If multiple files are specified, the content of these input files will be concatenated. This is very useful for generating a single pandoc output with input from different steps. We will demonstrate this feature in the Generating Reports tutorial.

If both script and input parameters are specified, the content of input files would be appended to script. So

In [9]:

Action Rmarkdown

Action Rmarkdown is very similar to pandoc, the only difference is that it uses RMarkdown to process the input, which is assumed to be of Rmarkdown format.

In [10]:
/Users/bpeng1/anaconda3/envs/sos/bin/pandoc +RTS -K512m -RTS tmp8j3g4tz4.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output /Users/bpeng1/sos/sos-docs/src/user_guide/out.html --email-obfuscation none --self-contained --standalone --section-divs --template /Users/bpeng1/anaconda3/envs/sos/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /var/folders/ys/gnzk0qbx5wbdgm531v82xxljv5yqy8/T//RtmpTVT462/rmarkdown-str13d6f78c71598.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /Users/bpeng1/anaconda3/envs/sos/lib/R/library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /Users/bpeng1/anaconda3/envs/sos/lib/R/library/rmarkdown/rmd/lua/latex-div.lua 

[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'tmp8j3g4tz4.utf8'

Output created: out.html