I am spinning up an instance of rstudio server and I need the working directory of R to be a specific directory. I would also like the file pane in the bottom right corner to be pointing to the same directory. Is there a way to do this? Currently it runs from the home directory of whichever user is running the program. I have tried the --server-working-dir flag, and it does not seem to work. Here is the command I am using:
/usr/lib/rstudio-server/bin/rserver \
--server-daemonize=0 \
--server-user=user \
--server-working-dir=/some/path \
--auth-none=1 \
--auth-minimum-user-id=0
Any help would be useful here.
[edit] Just wanted to clarify that I would like the server to start in this directory. I am building a container that will be deployed multiple times, and I don't want the users to have to set their directories every time it is deployed.
If you want to modify the file pane in the right, you should edit /etc/rstudio/rsession.conf.
And add two lines in below:
session-default-working-dir=/some/path
session-default-new-project-dir=/some/path
You can do this by edditing the (global) R profile startup script. Here's a step by step guide:
1) Run Rscript -e "R.home()" -- this will tell you the location of your R directory home. In my case (Mac) it is /Library/Frameworks/R.framework/Resources
2) Go to /Library/Frameworks/R.framework/Resources/etc -- e.g., $R_HOME/etc
3) sudo touch Rprofile.site if it doesn't exist, then sudo nano Rprofile.site
4) Add the following lines and save:
cat("hi\n")
setwd("/some/path/")
You should avoid overwriting the users home directory.
Amongs the [.Rprofile] files you should only edit the Rprofile.site as a last resort since it acts globally.
Suggested solution:
R read the "initialization file" at start, in the following order:
.Rprofile.site
.Rprofile (located in the current directory).
.Rprofile (in the users home directory).
In your case if you are planning to login to R-Studio server you will end up in the users home directory, so I would suggest you to just edit the [.Rprofile] in the home directory. In case the [.Rprofile] is missing you need to create it.
Add this line in your .Rprofile [in your home directory]:
setwd ('/your/path/')
Logout/login to your R-studio server session and you will notice that the "file pane to the right location" has changed accordingly to what you specified in your .Rprofile.
Related
I was wondering if there is a way to set a default folder every time I open JupyterLab. Is there any command I can run through Anaconda PowerShell Prompt? Or a JSON property I can modify in settings tab? Thanks in advance!
If you want to open specific file in directory a, say a/notebook.ipynb but then navigate the file browser to directory b, relative to the root directory, you can use file-browser-path query in the navigation URL (documented here):
http(s)://<server:port>/<lab-location>/lab/tree/a/notebook.ipynb?file-browser-path=/b
You can use this method from command line thanks to LabApp.default_url traitlet:
jupyter-lab --LabApp.default_url='/lab/tree/a/notebook.ipynb?file-browser-path=/b'
You can skip the opening specific file part:
jupyter-lab --LabApp.default_url='/lab?file-browser-path=/b'
If you want to change the root directory, please see this answer which explains how to do so with ServerApp.root_dir traitlet (in older versions of Notebook<7.0 and JupyterLab<3.0 used to be named NotebookApp.notebook_dir). Again, you can use it from command line, and even specify an absolute path:
jupyter-lab --ServerApp.root_dir='/home/user/project/'
# or on Windows say:
# jupyter-lab --ServerApp.root_dir='C/users/user/project/'
You can combine the two approaches, e.g.:
jupyter-lab --ServerApp.root_dir='/home/user/project/' --LabApp.default_url='/lab?file-browser-path=/project_subdirectory'
If you want to persist the changes (for either default URL or root dir), see the previously linked answer which details how to persist configuration.
Follow the answer . Just edit the alias alias my_jupn='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38 && jupyter-notebook --notebook-dir=/home/$USER/Documents/Jupyter_Notebook'
and for JupyterLab alias my_jupl='source /home/$USER/anaconda3/bin/activate && conda activate MyPy38 && jupyter-lab --notebook-dir=/home/$USER/Documents/Jupyter_Notebook'
N.B. Here MyPy38 is your active environment name. and if any error occurs then change $USER to your UserName. Lastly, /home/$USER/Documents/Jupyter_Notebook will be change according to your choice.
According to the jupyter.org:
I configured like this.
Terminal command active your envirnment by conda activate Your_env_name and then jupyter lab --generate-config. jupyter_lab_config.py should be created in dir /home/$USER/.jupyter directory.
Find
# c.LabApp.app_settings_dir = '' and uncomment.
Then give your directory like this.
c.LabApp.app_settings_dir = '/home/$USER/Documents/Jupyter_Notebook'
Similar for jupyter notebook. jupyter notebook --generate-config and then nu-comment and edit like c.NotebookApp.notebook_dir = '/home/UserName/Documents/Jupyter_Notebook'
**NB: /home/$USER/Documents/Jupyter_Notebook is my changed default dir. Change it according to your need. **
The command
jupyter notebook --generate-config
will create a config file.
The path to this file is displayed in your terminal or PowerShell.
Set the desired folder path as the string c.ServerApp.root_dir in this file and make sure you uncomment the line after you set the string.
Windows users will have to use double backslash in paths, e.g.:
c.ServerApp.root_dir = 'C:\\YOUR\\PATH'
I'm new to R and RStudio and am currently taking online classes to learn more about data science. In one of my lectures, I'm being asked to create a project in RStudio prior to creating a repository in github and linking the project with git. In order to make a pre-existing project interact with git, the instructions in my lecture are telling me to navigate to the directory containing my project file by using the "cd" command followed by the location of the file and file name. My project file is currently located on my desktop so I typed in "cd ~ /Desktop/temporary_no_version_control" however, the directory doesn't seem to change and remains set on the original location of the file which was in Users/savannahkeiffer. Just so I could complete the assignment, I re-located the file to my user file and tried to follow the rest of the instructions which told me to type "git init" followed by "git add ." which is where I run into the "warning: could not open directory" warning.
I have a macbook which runs on OS X Maverick. I went into my system preferences > security and privacy and selected Full Disk Access where I manually allowed terminal to have access to all the files on my laptop. However, after closing and re-opening RStudio and attempting the commands again, I got the same error.
This is what I entered when I tried to change the directory
Savannahs-MacBook-Air-2:~ savannahkeiffer$ cd ~
/Desktop/temporary_no_version_control
Savannahs-MacBook-Air-2:~ savannahkeiffer$ git init
Reinitialized existing Git repository in
/Users/savannahkeiffer/.git/
And what I got when I changed the location of the project on my laptop in order to complete the assignment (after already giving access to terminal)
Savannahs-MacBook-Air-2:~ savannahkeiffer$ cd ~
/Users/savannahkeiffer/first project/temporary_no_version_control
Savannahs-MacBook-Air-2:~ savannahkeiffer$ git init
Reinitialized existing Git repository in
/Users/savannahkeiffer/.git/
Savannahs-MacBook-Air-2:~ savannahkeiffer$ git add .
warning: could not open directory 'Pictures/Photos
Library.photoslibrary/': Operation not permitted
warning: could not open directory 'Library/Application
Support/MobileSync/': Operation not permitted
warning: could not open directory 'Library/Application
Support/CallHistoryTransactions/': Operation not permitted
warning: could not open directory 'Library/Application
Support/com.apple.TCC/': Operation not permitted
warning: could not open directory 'Library/Application
Support/AddressBook/': Operation not permitted
And so on.. Is this a directory problem or a "git add ." command problem?
It looks like what happened is that when you typed the cd command, you left a space in between the tilde and the rest of the path, so you changed back into your home directory (represented by the tilde). Then, when you tried to do a git init, you tried to initialize your home directory as a Git repository, and then ran into the fact that macOS restricts some programs (in your case, not Terminal, but maybe still Git) from accessing certain directories.
In the shell, the tilde is just a fancy way of spelling the environment variable $HOME, which points to your home directory (in this case, /Users/savannahkeiffer), so it should immediately precede the rest of the path without a space in between.
The best thing to do in this case is switch into your project directory and then initialize a repository there:
cd ~/Desktop/temporary_no_version_control # note the lack of space after the tilde
git init
If you didn't intend for your home directory to be a repository (i.e., you're not storing your dotfiles in a repository there), then you will probably also want to remove the .git directory from your home directory by running rm -fr ~/.git. Be careful when typing this, as rm removes data without prompting and an unfortunate space could result in all your data being deleted.
Hello this was an issue I had also but in Windows. It was a simple fix, user error. I hadn't used gitbash for awhile so I forgot the process with working in gitbash. First mistake I made was after opening gitbash I directly executed the git status command. That's when I got the "warning: could not open the directory" message. You need to using the cd (change directory) command and the dir (directory) command to navigate to the folder that has the files you want to "git add ." and "git commit -m". Once you get to that folder you will be able to use the "git status" command to see your changes then proceed as normal. I had to post this because it took me hours before I realized what I was doing wrong. No other stack post pointed this obvious user mistake. Hope it helps you.
I'd like to set the default distribution of Python for my Reticulate package to use. I use,
Sys.setenv(RETICULATE_PYTHON = "/usr/local/bin/python3")
however, I have to re-enter this line of code every time I start R. How can I set this permanently, so I don't need to specify which Python distribution I need every time?
On Windows, use Sys.getenv('R_USER') as #Brian Davis suggested in the comments to know the location of your home folder. On Linux, Sys.getenv('HOME') should be your normal home folder which you should use.
Now open up a terminal (if you're using recent versions of Rstudio there is one next to the console), go to your home folder and add a .Renviron file. You can do this without using the terminal too, but you'll probably have to confirm creation of a file starting with a dot.
cd path_to_my_home_Folder
touch .Renviron
Add RETICULATE_PYTHON = /usr/local/bin/python3 to it, and add also a new line at the end. Your file should look like this (if it's new):
> RETICULATE_PYTHON = /usr/local/bin/python3
Now you should be able to access your environment variable with Sys.getenv('RETICULATE_PYTHON') at each R session, since R looks for any .Renviron file defining environment variables in R home folder at startup (see documentation for startup?Startup).
UPDATE 29/10/2018
As it turnouts the variables defined with .Renviron are available only within Rstudio, which is not so much of a surprise since the .Renviron file is read at Rstudio startup. If you want the environment variable to be available for Rscript (for instance), you can :
Windows Add it to your user environment variables, using the Modify environment variables utility (available in the Start menu search bar)
Mac You can do the exact same procedure as above but do that on your .bash_profile instead of .Rstudio. Open up a terminal and place yourself to your user root folder (default location of the terminal usually). Add the following line (without blanks around the equal sign):
export RETICULATE_PYTHON=/usr/local/bin/python3
Save and close, restart terminal. The terminal reads your .bash_profile at start up, thus defining the environment variables. Your RETICULATE_PYTHON should now be available even in non-interactive R sessions.
The packge usethis has a function that opens the file .Renviron of your home folder.
usethis::edit_r_environ()
Once the file is opened, you just need add your pair key=value, save and close it.
RETICULATE_PYTHON=/usr/local/bin/python3
How to change working directory in Julia Jupyter?
I tried and read everything, still have no idea how to do that. It only allows me to select directories under my home ~/ dir. I can't find any button to go up to /.
I'm pretty sure once you have started the server you cannot then go up directories, I may be wrong though.
So best thing to do is start the jupyter notebook server somewhere that contains all of the folders you might need -i.e. the root dir if you want to make sure you have access to everything.
You can use the --notebook-dir flag for this. Or you can set defaults in the config.
you need to create the config file, using cmd :
jupyter notebook --generate -config
Then, search for C:\Users\your_username\.jupyter folder (Search for that folder), and right click edit the jupyter_notebook_config.py.
Then, Ctrl+F: #c.NotebookApp.notebook_dir ='' . Note that the quotes are single quotes. Select your directory you want to have as home for your jupyter, and copy it with Ctrl+C, for example: C:\Users\username\JuliaProjects.
Then on that line, paste it like this : c.NotebookApp.notebook_dir = 'C:\\Users\\username\\JuliaProjects'
Make sure to remove #, as it is as comment.
Make sure to double slash \\ on each name of your path.
Ctrl+S to save the config.py file !!!
Go back to your cmd and run jupyter notebook. It should be in your directory of choice. Test it by making a folder and watch your directory from your computer.
I use Jupyter Lab and start it from the Julia REPL (1.4) like this:
using IJulia
jupyterlab(dir=pwd(), detached=true)
Here's the scenario.
I am on the unix command line (in home directory). I want to browse the directory through
$ vim .
thus opening the vim netrw.
Now I am browsing the directory using the netrw.
What I want here is that when I exit vim netwr, I want my previous current working directory (in this example the home directory) to now become the directory I was previously in vim netrw.
Example:
step 1. now in home directory
step 2. vim . (thus opening vim netrw)
step 3. go to any directory (~/my/other/folders)
step 4. :q (to exit vim)
step 5. (here, I want my previous directory to now become ~/my/other/folders
any ideas on how to do it? I was thinking of doing something in .vimrc but I dunno how. Been into google search, but found nothing valuable.
A possible solution would be to change the current work directory while in netrw by pressing c, and spawn a new shell from the folder you're in by issuing :shell
So it would look like:
vim .
Navigate to the desired folder...
c
:shell
And there you are in a shell in the current folder you were in netrw.
And when you exit that shell, you fall back to where you were in netrw and can continue using the explorer.
I don't think it's possible at all. Every command executed via system('command') or :!command is executed through a subshell, not through the shell that started Vim so I don't see how you could alter the host shell in any way.
But I smell an XY problem here. What is your goal?
Do you want to be able to execute some commands on the files you just edited and you want to be in their directory? If so, do you know about :sh? :!command?
Do you want a "graphical" file explorer for your shell? If so, do you know vifm? Ranger? Midnight Commander?
To add to Wadih's answer, you can put this in your .vimrc file:
let g:netrw_keepdir=0
This means the working directory will be automatically updated and you don't need to press c each time.
So after navigating to a folder in netrw, all you need to do is do this:
:sh
And this opens the terminal in the current folder.
From the netrw help file:
By default, g:netrw_keepdir is 1. This setting means that the current
directory will not track the browsing directory. (done for backwards
compatibility with v6's file explorer).
Setting g:netrw_keepdir to 0 tells netrw to make vim's current directory
track netrw's browsing directory.