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.
Related
I am using pycodestyle_magic as a linter in Jupyter. I am following the instructions at
https://github.com/mattijn/pycodestyle_magic
But I get error with 1-cell checking be it '%%pycodestyle' or '%%flake8'.
1st ERROR
# 1st CELL
%load_ext pycodestyle_magic
# 2nd CELL
%%pycodestyle
a=1
print(a)
2nd ERROR
# 1st CELL
%load_ext pycodestyle_magic
# 2nd CELL
%%flake8
a=1
print(a)
1st ERROR
I'm basing this on your image you posted for '1st error' and not the inaccurate code you posted:
Note that the error in your first error was saying line magic and not cell magic because it was not looking for cell magic anymore. You can see it will look for cell magic on the first line of a cell by putting in %%fake_magic as a first line and then 2 + 2 as a second line of cell. Running that you'll see UsageError: Cell magic %%fake_magic not found.
Hence, your first 'error' is that you are missing that the first line of the cell where you want to use cell magic becomes special. You cannot have something else on the first line where you want to use cell magic, even if it is commented out. In the image, you have #%%flake8 above %%pycodestyle. If you remove that line, it should work.
2nd ERROR
I'm basing this on your image you posted for '2nd ERROR' and not the inaccurate code you posted:
You've stumbled upon a bug currently involving flake8. (Maybe same or more bugs seem to prevent the %%flake8 magic from working at all for now, see comments.)
The solution/workaround is very similar to the '1st ERROR'. Remove the line you were trying to comment out because it being there is causing an issue.
The reasoning appears to be complex about the way the %%flake8 cell magic appears to work behind the scenes so that you cannot have comments in the code content at this time or it won't work. (And the second time it sees that comment symbol, it throws the error you see.) This bug has been reported here.
But the solution/work-around for now is straightforward. Remove the complexity you added, and see if it works.
In case of the %%flake8 magic, running the demo notebook as shown there doesn't work as shown, and so there is indeed a bug in the current version that was introduced by actually a bug in flake8 that the extension uses, see the specific comment here and the link to the underlying issue over at the flake8 repo. (In fact the extent that it doesn't work may be greater than the notebook reflects because as discussed in the comments, even cells without commented lines fail to report any formatting issues. The demo actually doesn't have any without and so I got distracted noting it only didn't show the buffer error for the first one in the demo notebook but since it had a commented line I thought it was still related.)The other way to workaround it at present is to install an older version of flake8 as pointed out here. The solution was merged though and should be available soon, and so just avoiding the triggering code in simple cases like yours is probably easier.
Note about the inaccurate code:
Post code for what gave you the issue, not what you think gave you the issue. Part of why you are asked to provide code as text the way you ran it, it is so those looking into it can run it the same way. Plus they don't have to type and can easily run it as you did. Beyond that, there's more reason behind it: you can try to see if what you observed originally matches what you are seeing now.
If you had run what you posted under the heading '1st ERROR' as the code block text, you would have seen it without the error you showed in your image. Usually you'd then discern the error/difference yourself. In other words, starball's comment was trying to point you to why you should be doing that, and sorted that 1st error out yourself. That would ultimately make your point about the fragile nature of %%flake8 magic have more impact because it isn't diluted by report of an error that isn't really an error. Plus, you may have realized what was necessary to avoid '2nd ERROR' because that code block works without error no matter how many times you run it.
Technical notes:
Anyone wishing to try out pycodestyle_magic with some of this code and the demo notebooks can click here to launch such a session served via the mybinder.org. service with most things necessary already set up. Once the session starts up in the classic Jupyter notebook interface, you need to do some further preparation to use pycodestyle_magic. As detailed here, you can install it with pip install flake8 pycodestyle_magic. So open a new notebook with the Python kernel backing it using New drop down on the upper right side and then choose the Python3 kernel. When it opens, make a cell that has %pip install flake8 pycodestyle_magic and run it. Then put %load_ext pycodestyle_magic as a cell and run that. You can now try the magic with code or pull the demo notebooks over and run those.
My Rmarkdown scripts are getting quite large lately. Especially the code inside the R-chunk which makes over-viewing the whole script more and more tricky. Luckily in RStudio there's the functionality to close resp. minimize the code chunk to one line! However when chunks are becoming more, it takes time to close them all by hand.
Question: Is there a feature to close them all at once? Say when starting to work on the script and then reopen single chunks when needed.
PS: Wasn't sure to post this as a feature request on github or here.
Edit > Folding > Collapse All
Alternatively, (on Windows) Alt+O.
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.
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.
I am having some problems with my clipboard contents when using R. When I run my scripts/commands in tinn-r, very often I would get something that I had ran earlier pasted onto my R Console instead of the command that I have just selected.
To get over this, I would go to my clipboard and delete its content(text/syntax). However, the same text/syntax that I had just deleted would re-appear on my clipboard and would again appear on my R Console when trying to run a different syntax from my tinn-r.
Good luck. Tinn-R seems to be a particularly buggy way of interacting with R. Though it takes some effort to set up, the StatET plugin interface from Eclipse has been working way better for me than Tinn-R ever did.