chunk names must be unique between knitr documents in same directory

[v-a-s-a]

This may be a user error/workflow problem rather than an issue with knitr itself, but I was just burned by this.

If you have multiple knitr documents (say Rmarkdown files) in a single directory all chunks producing figures should have unique names between those documents! My workflow consists of writing .Rmd documents, converting those to regular Markdown, and using pandoc to produce a final PDF. From what I can tell, this is a pretty common workflow.

If .Rmd files produce figures with the same chunk name, then only the last figure produced remains in figure/. That means that all subsequent conversions from .md to .pdf reference only one version of a figure. This breaks the tie between the final document, and the code used to generate it.

It may be worth naming files in figure/ in such a way that they are explicitly tied to a report. Not sure what the cleanest solution would be: perhaps appending a short hash of the report file name to the .png file name. Alternatively, you could simple warn users that a file in figure/ already exists with that name and suggest they rename their chunk.

[yihui]

Thanks for the feedback!

That is exactly what the rmarkdown package does by default. Different .Rmd will use different figure/cache directories. You can also set knitr::opts_chunk$set(fig.path = ???) by yourself.

[v-a-s-a]

Thank you!

Also: spectacular work on this package. Its been enormously useful, and a lot of fun to use.

[yihui]

Thanks for the kind words! :)

[petrelharp]

I'd vote to re-open this, and take one of @vtrubets suggestions. This is a major gotcha, and just because rmarkdown does it right doesn't mean that knitr doesn't need to: there's good reasons to use knitr without rmarkdown on top of it.

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