[ESS] /bin/bash markdown : command not found

Ista Zahn |@t@z@hn @end|ng |rom gm@||@com
Mon Feb 23 18:33:47 CET 2015

I agree that exporting R markdown from emacs isn't as user friendly as
it is in Rstudio. That seems pretty typical -- usually things are a
little trickier in emacs compared to a special-purpose application.
That said, polymode should be able to do this (without needing an
external shell script) with polymode-export (usually bound to 'M-n e'
I think).


On Mon, Feb 23, 2015 at 11:48 AM, Paul Johnson <pauljohn32 using gmail.com> wrote:
> Thanks to everybody for clearing this up.  I did not realize there was
> another "markdown" processor besides pandoc.  How innocent I was.
> I never did figure out how to knit and then run the markdown program from
> Emacs markdown-mode, but after installing polymode, I find this much easier
> to understand because it has the 2 separate keystrokes to knit and process
> the markdown file.  That's a little inconvenient, but the polymode makes it
> super clear what's happening to the various pieces. And the second stage has
> a lot of choices concealed by the RStudio menus.  Some don't work right "out
> of the box" but they are surely encouraging.
> There's no denying that the RStudio folks have pushed ahead the dialogue on
> how to write markdown.  I don't like their editor very much, but I admire
> the effort to make a "one click" compile to presentation tool. The work in
> the rmarkdown package for R is truly impressive, they make a lot of moving
> pieces turn in the same direction. I've not found an Emacs-based way that
> works as well.
> Here's what I do to turn the markdown from Emacs into a presentation. Run
> this shell script.
> #!/bin/bash
> R -e "library(rmarkdown); render(\"$1\")"
> Here we stand on the shoulders of the rmarkdown package.
> On Linux, run "render whatever.Rmd" and that generates the output. Expect
> will be fine in Mac, only Windows is a puzzler now (since they have no
> standard "in the PATH" place for user scripts).
> I found it difficult to figure this out because RStudio makes this so easy.
> The RStudio "knit" button is doing the 2-step "knit + pandoc" render
> process. In case you are new to this too, I wrote out some notes to
> de-construct the steps.
> "RmdOnRmd" (clever title :))
>  http://pj.freefaculty.org/R/rmdonrmd/rmdonrmd.Rmd
>  http://pj.freefaculty.org/R/rmdonrmd/rmdonrmd.html
> Am having some trouble figuring the shortest path from start to finish for
> MS Windows users.
> Incidentally, one part of this I did not appreciate is that the RStudio
> template for Rmd presentations has the output specifiers in YAML. That
> "output: slidy_presentation" is not just asking for slidy, but a lot of
> slidy settings set by rmarkdown.  All of these can be customized, but I've
> not digested it yet.  I had one jolt.  The slide declaration
> ##A long slide {.allowframebreaks}
> is legal, but not compatible with all output formats.  So far, it only works
> with slidy_presentations. Too bad, ioslides_presentation output is a little
> more jazzy.
> pj
> On Mon, Feb 16, 2015 at 1:13 AM, Stephen Eglen <S.J.Eglen using damtp.cam.ac.uk>
> wrote:
>> >> Right now, I can open an Rmd file in Emacs, M-x markdown-mode, the
>> >> correct
>> >> menus appear. However when I try to compile something, I get the
>> >> minibuffer
>> >> error
>> >> /bin/bash: markdown: command not found.
>> >
>> > That sounds like a pretty clear hint that you should install markdown.
>> > But that will only give you .md --> .html, you will still need a way
>> > to convert .Rmd --> .md. One way or another most people are using
>> > pandoc for this, so you should probably install that too (if you don't
>> > have it installed already).
>> markdown-mode has a variable "markdown-command" which should point to
>> the binary (normally "markdown") that makes the html.  Get markdown or
>> try hooking pandoc in.
>> I am a fan of pandoc -- especially after I read this page:
>>   http://kieranhealy.org/blog/archives/2014/01/23/plain-text/
>> which shows how you can get citations into markdown.  I'm currently
>> writing a journal article with it, and the workflow is pretty nice.
>> LaTeX is still king but pandoc is great if ever you need html or .docx
>> from your source files.  One thing markdown currently misses is \label{}
>> and \ref{} equivalents, but there's discussion about implementing that.
>> Stephen
> --
> Paul E. Johnson
> Professor, Political Science      Assoc. Director
> 1541 Lilac Lane, Room 504      Center for Research Methods
> University of Kansas                 University of Kansas
> http://pj.freefaculty.org               http://quant.ku.edu

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