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I constructed a beamer_presentation .Rmd file in R Studio, and tried to compile it with rmarkdown::render(my_file). I am running RStudio Version 1.1.463; R Version 1.1.463 and Ubuntu 16. rmarkdown::render stopped RStudio with several errors (which I don't have access to now) and I needed to kill RStudio in the system. But once I had killed RStudio, my entire computer system; files, folders, everything but the operating system and app files were wiped from the system (including the R and RStudio settings).

Has anyone else had this experience? Unfortunately, I can't share logs, code or other informative items, because they have all been wiped. I restarted my machine, and the screen indicated that I essentially had a new install of Ubuntu 16.

I've had quite a number of operational problems with render and bookdown in the past, but nothing this extreme. I am posting to find if anyone else has had similar problems.

I've tried to reinstall backups, but my disks are scrubbed of anything except system files and folders. I have individual files on Google Cloud, but nothing that would help explain what happened.

I wish I could show code, but the disk is completely wiped.

I've been using R, RStudio and Ubuntu for several years, and never run into this ... I didn't expect this, and I would like to know whether this is an isolated case, or a more common occurrence.

user5373123
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  • I'm very sorry to hear that! I have heard similar problems (e.g. https://github.com/rstudio/rmarkdown/issues/1248 and https://github.com/rstudio/rmarkdown/issues/1095), but they are definitely this extreme. Are you sure you only called `markdown::render(my_file)` and didn't use other arguments? – Yihui Xie Feb 06 '19 at 21:13
  • Yihui, thank you for responding. There were no other arguments; I had output: beamer_presentation in my YAML header, and I was just experimenting. I can be more specific about the prior problems. I've never gotten render to work (I always use knitr on the RStudio pulldown menu). I've worked with it on an iMac, MacBook, Ubuntu 16 and 18 and never gotten it to work (most times it will run, but doesn't seem to do anything tangible). This time it really made a mess of things, and unfortunately I don't have access to any records that might provide insight into what happened. – user5373123 Feb 06 '19 at 22:28
  • My sincere apologies! I cannot think of a possible reason why `rmarkdown::render()` could wipe out everything on the disk (we certainly don't do `rm -rf /` in the package)... – Yihui Xie Feb 07 '19 at 03:54
  • Good motivation to use a backup app (I use bacula). Well, I'm certain you take precautions. I guess its just a "heads up" in case something like this shows up again. The bookdown package is very attractive so its been a bit of frustration that I can't figure out how to make it work as you document in the online book. At least I can get parts to work with knitr. – user5373123 Feb 07 '19 at 14:50

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