Images also need pandoc

[gaborcsardi]

CC @jeroenooms

Pandoc is in the SystemRequirements of knitr:
https://github.com/cran/knitr/blob/e3adb6f1d7b1ed4ae9c016c015c88e5a237f1d3f/DESCRIPTION#L90-L93

We already have an entry for it in sysreqs DB:
https://github.com/r-hub/sysreqsdb/blob/master/sysreqs/pandoc.json

Maybe Suggests is not used for finding system requirements?

[jeroen]

But from the log is looks pandoc, knitr and rmarkdown are all getting installed, and it still gives the warning.

@jimhester

[gaborcsardi]

@jeroenooms Oh, indeed.

[jeroen]

The build fails due to an xvfb problem by the way, not this warning.

[jimhester]

From https://github.com/yihui/knitr/blob/9394e12b764c9729368200a04dae770c098ab808/R/utils-vignettes.R#L8-L24 it needs pandoc-citeproc as well, which doesn't look to be installed on R-hub. https://builder.r-hub.io/status/magick_0.3.tar.gz-12769ec3c1339f46527af5bad4b3f1ca#L174 is the only mention in your build log.

[gaborcsardi]

I think knitr should explicitly specify that it needs pandoc-citeproc then. Anyway, I'll put in an exception for it in a minute....

[gaborcsardi]

Or do you think we should always install pandoc-citeproc, whenever we install pandoc? Maybe that's the best solution....

[jimhester]

@gaborcsardi I think you are probably correct, pandoc-citeproc should probably be in SystemRequirements: of knitr or rmarkdown (or both). These are really more like SuggestedSystemRequirements of course, but there isn't a defined field for optional system dependencies...

[gaborcsardi]

OK, I think we'll just install pandoc-citeproc (it is quite small) whenever pandoc is wanted.... but I need to update the sysreqs web app for that, because apparently it does not handle lists of packages....

[jeroen]

Crossposting here: yihui/knitr#1286

[gaborcsardi]

@jeroenooms wait, so the missing pandoc-citeproc is not the problem for us? I thought it was.

[jeroen]

I think in this case it is, but I am seeing this problem locally as well sometimes (and I have both...)

[jeroen]

Did you make pandoc-citeproc part of the default image? Then I'll try again if it now works...

[gaborcsardi]

Not the default image, but I'll just install pandoc-citeproc, whenever
pandoc is requested.

But this is not done yet, something in sysreqs does not handle package
lists, so I need to fix that first. I'll comment here, once it is done.

On Tue, Sep 6, 2016 at 4:42 PM, Jeroen Ooms notifications@github.com
wrote:

Did you make pandoc-citeproc part of the default image? Then I'll try
again if it now works...

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[gaborcsardi]

It should be OK now, pandoc and pandoc-citeproc go together.