Worth noting (as an associated issue), if you're using RMarkdown in RStudio
it overrides your working directory and uses/prefers relative paths.
There's more info here:
http://stackoverflow.com/questions/20060518/in-rstudio-rmarkdown-how-to-setwd

Mike

On 4 June 2016 at 10:09, Gerard Capes <[email protected]> wrote:

> Thanks both for the suggestions.
>
> Editing my Makefile to include the absolute path didn't fix things:
>
>
> Updating Pandoc manually did the trick. I was using the version from the
> package manager (and had checked for updates there, but only there).
>
> Thanks very much - saved me a load of stress!
>
> Cheers,
> Gerard
>
> --
> Gerard Capes
> Research Applications, IT Services, University Of Manchester
> 0161 306 2509
>
> Ten tips for writing excellent emails:
> http://www.expert-messaging.com/feedbacktips/
>
> ________________________________________
> From: Discuss [[email protected]] on behalf of
> Raniere Silva [[email protected]]
> Sent: 04 June 2016 08:04
> To: [email protected]
> Subject: Re: [Discuss] Can't get html to build from markdown [appeal for
>       help]
>
> Hi Gerard,
>
> >> Steps to recreate the problem:
> >>
> >> $ git clone https://github.com/gcapes/git-course.git
> >> $ cd git-course
> >> $ make preview
>
> I didn't had any issue. I also try
>
>     $ make -B preview
>
> and no problem.
>
> >> pandoc -s -t html \
> >>          --smart \
> >>          --mathjax \
> >>          --template=_layouts/page \
> >>          --filter=tools/filters/blockquote2div.py \
> >>          --filter=tools/filters/id4glossary.py \
> >>          -Vheader="$(cat _includes/header.html)" -Vbanner="$(cat
> >> _includes/banner.html)" -Vfooter="$(cat _includes/footer.html)"
> >> -Vjavascript="$(cat _includes/javascript.html)" \
> >>          -o 01-introduction.html 01-introduction.md
> >> pandoc: Error running filter tools/filters/blockquote2div.py
> >> tools/filters/blockquote2div.py not found in path
> >> make: *** [01-introduction.html] Error 83
> >>
> >> $ pandoc -v
> >> pandoc 1.12.2.1
> >> Compiled with texmath 0.6.5.2, highlighting-kate 0.5.5.1.
>
> Could you try update Pandoc to a newer version,
> https://github.com/jgm/pandoc/releases?
> The version you are using is a little old.
>
> Cheers,
> Raniere
> _______________________________________________
> Discuss mailing list
> [email protected]
> http://lists.software-carpentry.org/listinfo/discuss
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