When I'm using R notebook and always getting error message like
'pandoc.exe.. out of memory'.
And the code chunk seems to freeze and cannot be executed.
Can someone educate me how it works and why it happens? I tried to google the solutions. seems not that obvious. I wonder if there is any easy way to increase the 'notebook memory size'. I still have plenty of space on my ram...Thanks.
Related
it's been a few days that im trying to run my Rmd on Kaggle, but it simply doesn't work.
The main reason (I guess) is that, somehow the console is reading the code as an R code, but im sure that I'm using Rmarkdown.
Therefore, the console reads a Text line as a code line, giving me the code error below:
Also, i tried to copy and edit other's people markdown, but i keep getting the same error line.
You can check my code here: https://www.kaggle.com/badluckmath/kernel4c85aae59c/edit/run/39891200
He's working perfectly on my Rstudio.
I'm looking for a huge help here, please!
I've been stuck with this for a week!
If i press the buttom to run code, it will simply give me this error message.
For that, i still don't know the solution. But since this is a premade Rmarkdown and i knew that it works, i simple used the Save (Commit) options and at the end, it worked.
Seemingly out of nowhere, one of my Jupyter Notebook .ipynb files now takes forever to open, to the point where I receive Chrome notifications saying that the page is unresponsive. If I wait it out it does open, however. Once it does open, though, it fails to have any of its nbextensions applied. For example, I can now no longer use codefolding. The notebook also seems to have a fair amount of lag when I try to scroll or edit cells.
The file is 556 kB and does have its output cleared (as I've noticed that being an issue for others), though it does contain a few thousand lines of code. I'm able to open smaller files (391 kB) with far fewer lines of code quickly, with all my selected nbextensions active, and with no lag.
Why would this marginally larger file have such issues? What can I do about this?
EDIT:
I have noticed that when opening the file in question, my Anaconda Prompt outputs the following:
404 GET /nbextensions/widgets/notebook/js/extension.js
This error does not pop up when I'm running the smaller file. I'm confused as to why this error would be conditional on the file being ran.
EDIT 2:
The following link seems to be quite related to my issue:
https://github.com/ipython-contrib/jupyter_contrib_nbextensions/issues/822
Basically, it seems like the issue is simply that nbextensions don't play well with larger files. I'm going to try splitting up the code into multiple files and hope the core file becomes small enough for this to work out better.
See Edit 2.
Simple solution - just make the file smaller. Everything is working as expected now.
here are my console output examples
as you see, there are no output values when using r studio console.
Actually, there are many related issues about this, but no clear solutions. Only a temporal or Adhoc solution like: restart R or using r notebook script.
Anyway, this phenomenon happens just 1 day ago, with the same code, same operations.
At the first time, console works and a few minutes later it doesn't work.
It is so annoying me to restart or run r notebook script...
Is anybody have the same issues as me?
(I cannot give reproducible data, because it works well the other's computer)
Click on the gear icon beside knit and make sure that "chunk output in console" is enabled.
I ran into a very weird problem: my R code for generating a plot only works if I type it into the console but not when I ran it inside the script (with Ctrl+Enter command)... It's the same problem with all plots (regular plots or ggplots). Also I tried it on two different computers and the same thing happened. Anyone have any idea why this is happening?
One possible reason: I installed the newest version of Rstudio on both computers so it might be an issue with the version. The exact same code worked before on an older version of rstudio...Could this be it? If so, how can I fix it?
I think I figured out what the problem was: the setting in the new version of Rstudio has a default option of outputting the plots inside the Rmarkdown script (at the very end of the script). And that's why I wasn't seeing them. You could change the setting such that it outputs in the console.
Try dev.off() to reset the graphics device.
This helps with a lot of weird graphics behaviour.
Probably too late for the original poster... However, I just ran into the same problem after installing an R update. The way I fixed it was to go to preferences, R markdown, and turn off "show inline output". For me, it was just coming out at the bottom of the chunk instead of in the plot window like I wanted. Hope that helps someone!
I just ran into this problem. I mistakenly put my plot() command inside the r markdown setup chunk. I moved it to its own code chunk and it ran as expected.
When I run a large R scripts (works nicely as expected, basically produces a correct PDF at the end of the script (base plotting plus beeswarm, last line of script is dev.off()), I notice that the PDF is finished after ~3 seconds and can even be opened in other applications, long before the console output (merely few integer values and echo of code ~400 lines) is finished (~20 seconds). There are no errors reported. In between, the echo stops and does nothing for seconds.
I work with R Studio V0.97.551, R version 3.0.1, on Win-7.
gc() or close and restart R did not help, and the data structures used are not big anyway (5 dataframes with up to 60 obs and 64 numeric or short character variables). The available memory should be sufficient (according to task manager, around 4 GB throughout), but CPU is busy during that time.
I agree this is not reproducible for other people w/o the script, which is however too large to post, but maybe someone has experienced the same problem or even an explanation or suggestion what to check? Thanks in advance!
EDIT:
I run exactly the same code directly in R 3.0.1 (w/o RStudio), and the problem was gone, suggesting the problem is related to RStudio. I added the tag RStudio, but I am not sure if I am now supposed to move this question somewhere else?
Recently I came across similar problem--running from RStudio becomes very slow, even when it is executing something as simple as example('plot'). After searching around, this post pointed me to the right place that eventually led to a workaround: resetting RStudio by renaming the "RStudio-Desktop Directory". The exact way to do so depends upon the OS you are using, and you could find the detail instruction here. I just tried it, and it works.