Multiple Rmd files in subdirectories and common lib_dir

[gaborcsardi]

I have a bunch of Rmd files, spread in some subdirectories, e.g.

aaa/bbb/one.Rmd
aaa/ccc/two.Rmd
...

I want to convert them to HTML, and use a common lib_dir for all of them. The problem is, that if I do

render("aaa/bbb/one.Rmd", NULL, 
       output_options=list(self_contained=FALSE, lib_dir="lib"))

then the lib directory (and more importantly the the references in the generated HTML accordingly) end up in aaa/bbb/lib, which is obviously not what I want.

If I try

setwd("aaa/bbb/")
render("one.Rmd", NULL, output_options=list(self_contained=FALSE, lib_dir="../../lib"))

then I get

Error in relativeTo(basepath, dir) : 
  The path /private/tmp/lib/jquery-1.11.0 does not appear to be a descendant of /private/tmp/aaa/bbb/

Is there a way to create a common lib_dir for these files, and still get the links in the HTML files right?

[andreasio]

FYI: I went to stackoverflorw with this issue. No answer yet though.

[gaborcsardi]

One workaround is to create a (symbolic) link for each lib directory output, that points to the real lib directory. The files are still written many times, of course.

[jjallaire]

The current design assumes a single root directory for documents that want to share a lib_dir. It would be pretty involved to reverse this assumption, so I'd recommend you do something based on symbolic links for now.

[gaborcsardi]

In the example above, the files are in a common root directory, aaa, and the problem is that lib_dir is not created relative to the common root directory, but relative to the Rmd file.

So it seems that in addition to a common root directory, you need to have all Rmd files in the same directory. Maybe this is what you meant by common root directory.

[jjallaire]

Yes, that's exactly what I meant.

On Thu, Jul 10, 2014 at 12:50 PM, Gabor Csardi [email protected]
wrote:

In the example above, the files are in a common root directory, aaa,
and the problem is that lib_dir is not created relative to the common
root directory, but relative to the Rmd file.

So it seems that in addition to a common root directory, you need to have
all Rmd files in the same directory. Maybe this is what you meant by common
root directory.

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#146 (comment).

[sjackman]

👍

[sanjmeh]

This is a strange restriction.

If I have understood it correct, the lib_dir is expected to be in the same directory as output_dir argument of rmarkdown::render(). This is a big limitation as it forces all the output html files to be saved in the same parent directory where the .Rmd is present. If we want to use the same .Rmd to generate a separate bunch of html files (based on the argument output_dir), we cannot share the same lib_dir. I have 50+ html files generated in every pass, and cannot abandon the subdirectory structure. Do we have a solution to this?

[jonathan-g]

I have the same issue.

I organize my reveal.js slides for a semester in a directory structure:

semester:
    lecture_lib (common material: css, js, etc.)
        assets (custom css themes, custom js, etc.)
        revealjs
        font-awesome
    slides
        class_01
            assets (per-class assets)
                images (images to include)
                videos (video files)
                fig (figures generated by RMarkdown)
        class_02
            assets (per-class assets)
                images (images to include)
                videos (video files)
                fig (figures generated by RMarkdown)
        c;lass_03
            assets (per-class assets)
                images (images to include)
                videos (video files)
                fig (figures generated by RMarkdown)
        ...

This lets me keep a consistent structure for each lecture.

This worked fine with RMarkdown for several years until Pandoc 2.9, when modifications to html_dependencies() broke my structure because RMarkdown insists on creating a file header-attrs.js and I am not given an option of specifying a path to a static version of header-attrs.js.

If I use pandoc 2.7.x, RMarkdown works fine with my directory structures, but if I use any later version of Pandoc I get the same error message about relativeTo().

[cderv]

@jonathan-g , this is a pretty old issue (2014).
Can you open a new one (linking to this one if you think this is related) with a reproducible example (would be ideal) ?

The fact that something broke with new pandoc make me thing there is something to fix.

Thank you !

[jonathan-g]

Sure.

[sjackman]

Could you please post a link to the new issue here?

[jonathan-g]

I just submitted a new issue #1859. I took some time to investigate this more carefully and to write up the new issue carefully before submitting it. I think a small PR can enhance rmarkdown to support this kind of non-standard directory structure (see the fork at https://github.com/jonathan-g/rmarkdown/tree/minimal-tree-fix).

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