"long vectors not supported yet" error in Rmd but not in R Script

Question

I am operating matrices with R 3.1 and RStudio 0.99.

I have my R Script and with cmd+enter it works without problem.

I created an Rmd for reporting but I have this error

Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,  : 
  long vectors not supported yet: ../../../../R-3.3.1/src/main/connections.c:5600
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> lazyLoadDBinsertVariable
Execution halted

Is there a way to bypass that error?

This seems to be a dupicate of Large Matrices in R: long vectors not supported yet

but the difference is that this only happens when trying to create an Rmd, not in any other case

Robotize

how many no of observations are you working with? – Factory

Possible duplicate of Large Matrices in R: long vectors not supported yet – Megacycle

it is a 28630x50247 matrix but the error only appears with the Rmd – Robotize

Also check this: github.com/yihui/knitr/issues/572 – Megacycle

Answer 1

I also ran into this today, and fixed it by using cache.lazy = FALSE in the setup chunk in my .Rmd.

So what is inside of the first chunk in my R Markdown file looks like this:

library(knitr)
knitr::opts_chunk$set(cache = TRUE, warning = FALSE, 
                      message = FALSE, cache.lazy = FALSE)

Dade

This is the right answer. I just wanted to add that for whatever reason, I had to access it from options instead of opts_chunk$set. So I had options(cache = TRUE, warning = FALSE, message = FALSE, cache.lazy = FALSE). I'm on RStudio 3.2.2 if that makes any difference – Tanika

This is probably sue if you are caching a very big R object. That was my problem. – Dalhousie

Using the original answer with knitr::opts_chunk$set worked for me on R 3.5.1. – Gamecock

For more background read bookdown.org/yihui/rmarkdown-cookbook/cache-lazy.html – Helainehelali

Answer 2

I am getting the same error in my .rmd file while trying to knit it to pdf. The incriminated code chunk was cached.

Is there a way to bypass that error?

Removing the 'cache = TRUE' or setting it to FALSE seems to fix the issue.

Ochs

This does not provide an answer to the question. Once you have sufficient reputation you will be able to comment on any post; instead, provide answers that don't require clarification from the asker. - From Review – Salacious

Hi. I wasn't caching. I cached now and it happens with or without caching. A possible solution was already commented. – Robotize

Thank @Salacious for the clarification. I don't get why I am being downvoted because the solution I suggest actually fixed the problem for my script. – Ochs