I'm running R as another user on my system (sudo -uTest R), and certain commands (e.g. plot) fail with 'unable to open connection to X11 display'. This works fine running R normally, so I know it has to do with running as someone else. I'm guessing this happens because Test doesn't have the desktop/display/whatever running under their name so there's nowhere to draw the graph.
Is there anything I can do about this?
In a terminal window, type:
xauth merge /path-to-your-home-directory/.Xauthority
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I am used to using R in RStudio. For a new project, I have to use R on the command line, because the data storage and analysis are only allowed to be on a specific server that I connect to using ssh. This server doesn't have rstudio-server to support remote RStudio sessions.
The project involves an extremely large dataset, and some pre-written code to load/format the data that I have been told to run using "source()" before I do anything else. This takes several minutes to run and load the data each time.
What would a good workflow be for something like this? Editing my code in a .r file, saving, then running it would require taking several minutes to load the data each time. But just running R in an interactive session would make it hard to keep track of what I am doing and repeat things if necessary.
Is there some command-line equivalent to RStudio where you can have an interactive session but be editing/saving a file of your code as you go?
Sounds like JuPyteR might be your friend here.
The R kernel works great.
You can use it on a remote server either with exposing an open port (and setting up JuPyteR login credentials)
Or via port forwarding over SSH.
It is a lot like an interactive reply, except it holds state.
And you can go back and rerun cells.
(Of course state can be dangerous for reproduceability)
For RStudio you can launch console and ssh to your remote servers even if your servers don't use expensive RStudio for servers platform. You can then execute all commands from R Studio directly into the ssh with the default shortcut key. This might allow to continue using R studio, track what you're doing in the R script, execute interactively.
I am a professor at a small college, and I am working with a blind student in a statistics course. We have found that R is by far the most accessible system to use, and for the screen reader to work (i.e. for it to read the output), we need to run R out of the Command Prompt (the student uses a Windows machine, specifically one running Windows 7). Though using the R console would probably be easier to operate, for some reason the screen reader being used by the student (JAWS) doesn't read the output in the console.
We have gotten to the point where we can use R out of the Command Prompt just fine, but the issue is that we cannot save the command history and the output from the Command Prompt to an external file (e.g. a .txt). I understand that I can use the sink() function to get the output in a .txt file, and I can also use the savehistory() function to get the command history, but I need something that captures both. We have also tried to use CMD outside of the R environment to try and print the full session of the Command Prompt, but that doesn't seem to capture the work that we might do during an R session.
On a Mac, this wouldn't be a problem, but I am not the best with using the Windows Command Prompt.
Any help would be greatly appreciated, and if more detail is required, I am more than happy to provide it.
sorry if this question is not as detailed and focused as it should be.
I am a Linux user (so no admin privileges of any sort) and just installed Anaconda3 from here and followed the instructions.
Note that my Linux machine is not connected to the internet, so I had to transfer the file through other means and just run bash Anaconda... as instructed in the Continuum site.
I have then succesfully launched IPython and tried to plot inline, without problems. However, when I tried to use plotting in windows, I got this kind of output from the terminal:
X Error: BadDrawable (invalid Pixmap or Window parameter) 9 Major opcode: 62 (X_CopyArea)
And the created graph window was just blank.
I then tried to start Spyder and basically saw the same behaviour: a lot of those errors reported above, and the Spyder window just popped up blank.
Google search for the error gives results reported for Qt, which makes sense since when plotting "offline" (as opposed to inline) then QtAgg is used.
However, I have no clue as to where to look for the version of these libs, how to install/compile new ones, whether that is really the issue or not. I am just to ignorant about Linux.
Anybody can hint on what to look for and how to try to debug this behaviour?
I had the same error. What worked for me is to add this line in /etc/environment.
sudo nano /etc/environment
Add this line
QT_X11_NO_MITSHM=1
Source : https://github.com/P0cL4bs/WiFi-Pumpkin/issues/53#issuecomment-309120875
Note that in my case the fix didn't take effect until I rebooted my machine.
you may simply run on the terminal:
export QT_X11_NO_MITSHM=1
I had this same error, so I'll tell you what worked for me.
I think it is a permissions issue, based on the following:
I was logged in through a VNC server window through my account, but within the VNC server was setting up a user profile for "user2". In a 'user2' console I installed anaconda in user2's directory. When I typed spyder in the user2 console, I got the exact error you describe. I guessed the VNC desktop didn't like user2 trying to open a window on user1's profile. I then logged out of my VNC server window, logged into the user2 vnc server window, and in a console typed 'spyder' and it opened perfectly.
I think for some reason it is trying to open but is installed in a directory that you don't have permissions for or trying to open in a window that you don't have access to.
When I access the RStudio (hosted on a server) shell (Tools > Shell...), I gain admin access by using sudo R, then typing my password, which I know is invisible for security reasons. However, every subsequent line of code I type is also invisible.
For example, say I want to download a package to make it available on the server. I use:
install.packages("spls", lib="/usr/lib/R/library")
The above text does not show up, but when I press Enter, it does execute and I'm asked for a mirror to use. The package then is correctly installed. Thus, the only problem is not being able to see the text. This happens for anything I type in the shell.
I'm not the host of the server, but I do know it uses Ubuntu, I believe the RStudio version is 0.99.473 and the R version is definitely 3.2.1. I'm running on a Mac with Yosemite and Safari. If more specific information would be helpful, I can contact the host.
Does anyone know what might be causing this issue and how to fix it?
I've got a lengthy process running in Rstudio and I would like to open a separate session of Rstudio while the first one is running. I know I can run R from the command line to get as many sessions as I want, but I wanted to know if it is possible for me to do this in Rstudio on a Linux computer. Thanks.
#infominer suggested a good solution, which is to simply type rstudio in the command line. That's what I ended up doing
Another convenient way to deal with this is to start a seperate R-instance in the terminal by typing simply
R
and from there just run the script that has a lengthy process with
source("path-to-your-script/your-script.R")
you can than continue to edit and work with your two scripts in the already opened R-Studio editor window.