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quantitative-biology / Basics

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yaml problems? #1

Closed kcudding closed 3 years ago

kcudding commented 3 years ago

don't think the "../module-1-git/module-1-git-intro.Rmd", line is correct in the yaml? That file doesn't exist as far as I can tell? However, I can't compile at all now, so not sure where the error is

kcudding commented 3 years ago

after removing those files from _bookdown.yaml I can compile...

andrew-edwards commented 3 years ago

You need to git clone the other modules. I did it like this so people can still render an individual module in it's own directory. Or commenting out like you did will do it. I added something to the quant-bio README yesterday.

We probably want to move all the modules to this repo at some point.

kcudding commented 3 years ago

So, I DID do that. I have cloned all the modules. And 3 and 5 are in their own directories, and they work.... but of course I can actually see the .RMD file in those cases, could not see module-1-git-intro.Rmd in the directory /module-1-git

kcudding commented 3 years ago

But I can see on github now... where they there last night?

kcudding commented 3 years ago

new pull from module-1 now gives "You have 7 Rmd input file(s) but only 6 first-level heading(s). Did you forget first-level headings in certain Rmd files?"

And it does indeed look like there might be missing bits in module 1

andrew-edwards commented 3 years ago

I'm ignoring those warnings for now. I think the idea is that you have just one .Rmd for each Chapter (each module in our case, plus an Intro maybe). We don't have that right now, but it doesn't seem to matter. I have my Git stuff currently split over three files, but as long as they called in that YAML file it doesn't really matter I think. We can tidy up warnings at the end.

andrew-edwards commented 3 years ago

Think we can close. There are some warnings but they're fine.

andrew-edwards commented 3 years ago

@kcudding - I did notice there's some YAML stuff at the start of your two modules (I think). Probably not needed (since bookdown and it's all at the start), but everything seems to work so probably not worth messing with either.

kcudding commented 3 years ago

?? I have no yaml stuff. I do have some r chunk stuff, is that what you mean? @andrew-edwards

andrew-edwards commented 3 years ago

Hmmm... you're right. Maybe it was this that I saw: https://github.com/quantitative-biology/module-5-optimization/blob/main/Module5_solutions.Rmd though if it's not part of the build then that's fine. I'll close.