I am using JupyterLab to build a bioinformatics pipeline that uses both bash and python scripts.
The first bash script results gives a lot of feedback on every step of the process. However, this feedback is not helpful (unless there was an error) and makes the document less readable.
I would like to be able to hide this cell's output by default, but also to be able to open it when necessary to troubleshoot. I know it's possible to click 3 times on the output to collapse it; I was just wondering whether there is a way to do so by default.
I tried to add the tag specified on here (https://jupyterbook.org/features/hiding.html#Hiding-outputs) to the cell, but it does not seem to work for me.
Thanks for your help.
You may just want to suppress the output using %%capture cell magic as illustrated here. Then you simply remove that magic command from the first line of the cell for times you want to see the output, such as when troubleshooting.
If you want to make it so every time you run the cell, you can later decide to review what was captured you can use the %%capture magic command more as it was meant to be used. By assigning what is captured you can also do something like what the %%bash cell magic allows with handling output streams (see here), too. As described and illustrated here using the utils object you can easily get the stdout and/or stderr as a string, see http://ipython.readthedocs.io/en/stable/api/generated/IPython.utils.capture.html.
So say you put the following at the top of you cell to assign what was captured to out:
%%capture out
You can review the stdout stream later with the following:
print(out.stdout)
Or if you just want part of it, something like print(out.stdout[1:500]). I have some fancier handling illustrated in some blocks of code here.
I, an R user, decided recently to try using Emacs-ESS combo. So far I have been work in a single-window mode (C-x 1) just for text highlighting.
Now I am trying split it in two windows (C-x 3) to work on an .R file in the left window, and have R execute the commands in the right window. Something like this:
After selecting sections of code on the left, how can I "send" it as a command to the right? Essentially, I want the input to remain on on the left (so that I can incrementally build the code up) and the actual R output on (including error messages) the right.
Two good options:
ess-eval-region-or-function-or-paragraph vis
(C-M-x): Sends the current selected region or function or paragraph.
ess-eval-region-or-function-or-paragraph-and-step (C-c C-c): Like ess-eval-region-or-function-or-paragraph but steps to next line of code.
Source: ESS manual.
You can also use:
C-c-p to send a paragraph or region between two empty lines
C-c-r to send a region that has been selected and is highlighted
I prefer this way because you only need to press the Ctrl key
there are normally many ways to send code to the R console. It will take you time to realize what is best for you, or you may eventually change the key bindings.
Suddenly R Studio stopped auto completing my list and data frame contents when entering mylist$ then pressing Tab. The result message I get is
No matches
I tried that on very simple lists or data frames like:
simpledataset <- data.frame(a=rep(0,100),b=rep(1,100))
However, when I load the dataset Mtcars, it correctly shows the column names.
I reset %localappdata%\RStudio-Desktop by renaming it, but didn't change anything.
Any idea of what could be the cause of that?
This sounds like a bug in the autocompletion system that is occasionally triggered when certain packages are loaded, or the byte-compiler optimization setting is increased. You might try checking a few things:
What is the value of compiler::getCompilerOption("optimize")? Autocompletion is known to fail when this value is equal to 3 in the current RStudio release (v0.99.896). You can try running compiler::setCompilerOptions(optimize = 2) to resolve this.
What packages do you have loaded? You can try loading packages one-by-one to see which affects RStudio's ability to provide autocompletions.
Finally, there should be a fix for this in the preview version of RStudio -- you can try it out at https://www.rstudio.com/products/rstudio/download/preview/.
Go to Tools>Global Options... and set autocomplete there.
The problem is that when I run the code, there's no return in the console; I mean it does run the code, but does not return any output.
For example, if I write
v <- c(1, 2, 3, 4, 5)
v
I would expect in return
[1] 1 2 3 4 5
But it's not working.
I have version RStudio Version 0.98.1079 and R Version 3.1.1
Possibility 1 (until the + sign was mentioned): I was wondering if you had been doing a tutorial where they were demonstrating the sink function and you hadn't gotten to the point where it was reversed.
> sink('out.txt') # diverts all output to a disk file
> v <- c(1,2)
> v # output went to file
> sink() # sets the output back to the console
> v
[1] 1 2
Another way would be to call closeAllConnections:
> sink('out.txt')
> v
> v
> closeAllConnections()
> v
[1] 1 2
Possibility 2: To address the lack of response with a "+" showing at the Rstudio console ... that is a sign that the R parser "thinks" the entered text has not completed a full R command. It may indicate that you haven't typed a closing bracket or parenthesis. If typing one or two of those is unsuccessful and you keep getting mor +'s then you may be successful with typing the [esc]-key. If it is showing up immediately after a restart then you should check your code for correctness and make sure that the .Rdata file is deleted from your working directory. If you don't know what that means then you may need to search for the methods appropriate to your operating system. You could also have an error in the code of one of your .rprofile files.
In any case these two possibilities have nothing to do with Rstudio per se and everything to to with the typical behavior of an R console session in pretty much any IDE.
Do the lines still start with a "+"? It is also possible you forgot to close the brackets of a function. Try "}".
I had the same issue and none of the tips mentioned here were working.
Session > Restart R did the trick for me, possibly suggesting that I had a similar problem as andrewH but was not patient enough to wait for R to behave again.
This is a very old question, but I just had the same problem with a different cause, so I thought I would describe it here case it should be useful to someone else. I was getting the regular command prompt, with nothing more, no matter what I typed at the command line. I tried multiple returns, escape, sink, traceback, closeAllConnections (which did give me a response, "error: unexpected ) in (), but then went back to the command prompt and ignored a second traceback).
Anyway after half an hour or so of pulling my hair out, up pops "View(Mid2)". Mid2 is a tibble with 8.5 million observations of 88 numeric variables. I must have tapped it in the environment pane accidentally. I suppose it just took that long for the viewer to render it. I assume that all the other things I did hit at once, because RStudio crashed immediately thereafter.
The interesting thing about this particular version of the problem is what didn't happen. The red stop sign in the upper right of the console window, that lights when R is busy, didn't light. That is unfortunate -- but understandable, if the RStudio viewer is a different process. But also, when my computer is working hard on a really big computation or IO task, the fan usually starts, but it didn't. Don't know why. . I took its absence, incorrectly, to mean no such computation was underway.
If the lines in console are starting with "+".
Save your work and close the 'RStudio' or other tool which you are using and Start it again, it worked for me.
If you are using R Studio Cloud, refresh or re-opening won't work.
Only clue from the above posts or answers is your console will always start with '+'
In my case I tried all possibilities of closing braces.
And ")" worked for me when I typed that into the console and press enter.
sink() function did nothing in R Studio Cloud
A simple mistake might have also caused this problem:
A rather lengthy command left abandoned in the console is blocking the appearance of the result line.
Thus, the console only shows that line, but the result from any code run from the source, will not appear.
To solve this, just switch to the console, remove any remaining command and try again.
Experiencing something like that explained here as an unresponsive console to the R-Code running was just devastating for me when I experienced it. But luckly although I tried every trick explained in this page, it did not work for me. At last I clicked on the "To console" option available just below the Environment, History, Connections, Tutorial Tab on the R Studio. It solved the puzzle for me just now.
The best solution I've found is closeAllConnections and/or sink which almost always work
But as a stop gap measure, View()'ing always works. It's sort of a pain but whatever you wanted to print out, surround by View and you can see it
I know the sink command can divert the stdout to a file, but basically if I do this in the command window:
library(data.table)
a = 1;
b = 2;
a
[1] 1
Only the last line [1] 1will be printed in the file.
Is there a way my whole command window could be printed to a file like it is done with sink ?
NOTE: I want it to be done each time I write something to avoid losing everything if R crashes, meaning I do not want to have to type printAllCommandToFile() for this to be done
What about txtStart from the "TeachingDemos" package? See here.
Sometimes, when introducing students to R, I've recommended it to help them remember what they did and what the results were, a situation somewhat like you describe.
In my experience on a Linux machine, even if you close R without calling txtStop, the output is saved to whatever text file you had specified at the start of your session.
You do not say what environment you are in. On my machine (Mac) I can type cmd-A (for select-all) and cmd-S (for save to file) and get a save-dialog. Pretty sure something similar exists on Windows and *Nix devices as well.