debugging options with rmarkdown

Question

I am using the rmarkdown with the rshiny for generating word file reports. I am using the R studio-server for development. On executing the rshiny application, it halts due to some error in the one of the rmarkdown. The error says...

Quitting from lines 11-486 (/home/KS127/dev/shiny_apps/pashiny/inst/shiny/dataframe_source.Rmd) 
Quitting from lines NA-486 (/home/KS127/dev/shiny_apps/pashiny/inst/shiny/dataframe_source.Rmd)

It's providing the line numbers which are not useful to identify the root cause. Adding print statements are also not useful as I am generating the word file report, until and unless the complete .Rmd doesn't get successfully executed, I won't be able to see print statements output.

I tried changing the rmarkdown output setting from chunk output inline to chunk output to console as mentioned here as well but it is of no use.

Is there any way to print the .Rmd file print statements or the output to the console or is there any way to debug the .Rmd file?

Just keep commenting lines out until you find it. Binary search. That is what I do... — Mike Wise, May 12 '17 at 11:47
You could follow this tweet and move the chunk in question around in your code: https://twitter.com/jennybryan/status/665273964130795520 — p0bs, Jun 01 '17 at 12:33
@p0bs Surely I will give a try to this one and update my observations here. — Abhinandan Satpute, Jun 01 '17 at 12:46

score 2 · Accepted Answer · answered Jun 02 '17 at 10:12

2

In addition to my comment above, Abhinandan, I've recently stumbled across a new package, called testrmd.

Although it is new, it seems to work with a number of different test packages and provides a useful front-end for Rmarkdown documents. (I'm certainly going to use it.)

You might want to check it out. Here's the link: https://github.com/ropenscilabs/testrmd.

I hope this helps you.

answered Jun 02 '17 at 10:12

p0bs

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It is helpful. I am exploring it's features. – Abhinandan Satpute Jun 05 '17 at 11:54
Pleased to hear it – p0bs Jun 05 '17 at 12:05

score 0 · Answer 2 · answered Nov 04 '19 at 18:56

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See My .Rmd file becomes very lengthy. Is that possible split it and source() it's smaller portions from main .Rmd?

That's what I do. - Split your code chunks in separate files and add them one by one

answered Nov 04 '19 at 18:56

IVIM

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debugging options with rmarkdown

2 Answers2