rstudio hangs on knit, no error message

knitr

#1

I have a RMD file that starts off by importing data. Right now, while debugging this is the ONLY thing in the rmarkdown file (aside from the YAML header)

load("data/nesarc_rdata.RData")

This is a "large" data file, 43k records, 3k variables. 20M on disk.
If I run this code interactively, it works fine. Data is read in - hooray.
If I knit, no errors show up, but the program hangs when it hits that code chunk. And that stop sign icon that shows up in the top right of the Rmarkdown window, goes away shortly. Then... nothing.

It is specific to this data set, BUT it works on my local desktop version. This is not unique to my project, I am trying to debug problems for some of my students.

If I open the project and call rmarkdown::render() on the RMD file in question it works, but only the first time. If I change nothing, and called render again, and it hangs.

I am at a total loss as to how to debug/proceed. It works with other data sets, and it works when commenting out load() and knitting the same file.


#2

I would restart R before rendering the same documents again. I get the same issue doing something very similar on the desktop.


#3

But I never restart R studio before knitting.
I always re-knit my documents many times. I specifically instruct students to do knit early and often to catch problems in the code.

And it doesn't address the problem that clicking "knit".. fails with no error message. It just stops.


#4

Sorry you are having issues. Currently there is a 1GB memory limit on the container in cloud and when that is hit the R session will be killed in a way fairly similar to what you are describing. If you can send me the URL for the project I can confirm the issue in our logging.

Sean