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I think that is simply due to the fact that Pandoc was not available when the vignette was built, in which case knitr falls back to R Markdown v1 (the vignette you showed on CRAN was built with v1). If you build the package inside RStudio, you should be fine; otherwise you will have to either make symlinks of RStudio's pandoc and pandoc-citeproc to your PATH, or install Pandoc separately.
-- great. I think so. It works well in RStudio (as the R Markdown V2 Vignette page said). Probably I should wait for CRAN to update its package building infrastructure, until then, I guess I might need to use some workaround.
You don't need to wait for CRAN. CRAN uses whatever vignette output files you submitted in your source package. They don't rebuild vignettes. The problem must have come from your source package. As I said, if you build the package in RStudio, you should be fine, otherwise make sure pandoc and pandoc-citeproc are on your PATH.
@yihui -- yep. I finally figured it out. It's my problem -- installed Pandoc version was too old.
The interesting part -- the reason why I didn't notice this: I thought I installed pandoc via Homebrew, which means it will get regular updates via brew update / upgrade. However, Pandoc was actually installed via official binary installer, which means I haven't got a single update of Pandoc for two years ... Thanks for @meriops I got to notice Pandoc's version issue.
It is also shocking for me to know that CRAN will not rebuild vignettes. I think a problem like this is exactly why they should rebuild vignettes.
Personally I dare not suggest additional work to CRAN maintainers, so I think it is fine that they just use our pre-built vignettes, which saves trouble of both parties (package authors have control over what to display on CRAN, and CRAN maintainers don't need to install and maintain Pandoc).
That's reasonable. It will not be easy to change this tradition, for both sides ...
Thanks for sharing this. Since I did notice there were delicate differences between the rendered results of different Pandoc versions, I guess it's necessary to keep this in mind (also in configuration).
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