I am working with a "factory fresh" version of RStudio on Windows 7. R is installed under C:/Program Files which means the default libraries are stored here, and the two locations contained in .libPaths() on startup are both within this folder.
I want to work with another R library (igraph). Since the C:\Program Files folder is write-protected, I have set up another area to work in: C:\Users\nick\R and installed the igraph library in C:\Users\nick\R\library. I can manually add this location to the .libPaths() variable and use the library with no problems.
However, my problem is getting RStudio to automatically add this location to the .libPaths() variable on startup. I read that I could add the relevant command to my .Rprofile file - but I couldn't find any such file (presumably they are not automatically created when RStudio is installed). I then created a file called .Rprofile containing only this command. This only seemed to work when the .Rprofile file was saved in C:\Users\nick\Documents (which is the path stored in both the R_USER and HOME environmental variables). What I would like is to have the .Rprofile file stored in C:\Users\nick\R.
I have read all the information in ?Startup and it talks about where to store commands that run on startup. But I just can't make this work. For example there seems to be no way to change the location of the home directory without reading a file stored in the home directory. I don't seem to have any .Renviron files and creating these myself doesn't seem to work either.
I would really appreciate an answer in simple terms that explains how I could go about changing where the .Rprofile file is read from.
In Windows, you set the R_USER profile by opening up a command line and running:
SETX R_PROFILE_USER "C:/.../.Rprofile"
Where (obviously) the path is the path to your desired .Rpofile. In R, you can check that it worked:
Sys.getenv("R_PROFILE_USER")
Should return the path you specified. Note that you likely need to have all R sessions closed before setting the R_USER variable.
Related
I have a series of pieces of R code which have been designed to be run on other computers. That is, all code is relative to a root directory, which contains a Rstudio project file, .Rproj. There are no absolute file paths. This works fine when I actually open Rstudio, load the .Rproj file and then run the code.
However some of my code takes hours to run, and I need to set multiple scripts to run one after the other. This means creating a .sh file, and running the R script in turn from the command line. However non of my programs run successfully from the command line, as the root directory is no longer set to that of the .Rproj file. I have read about the here package can be used, which will automatically set the root directory to where ever a .here file is located. This is not the case for me.
The working directory it automatically uses is the home directory I have on the computational cluster I am using. The area where all my files, including the .Rproj and .here files is located in a different directory in which I have a lot more space allocated. Both are accessible from a common parent directory, so I assumed there here() function would be able to locate the directory I want to actually use to run my work. But this is not the case.
Effectively, I would like to set the root directory to a location which is not the default root directory on the system I am using. I have put a .here file there, but this is not located by there here() function, which I believe is its primary objective. Any ideas on how to proceed?
EDIT: I am working on a UNIX system. R version 3.4.2.
My problem was similar, but not exactly the same as yours. Perhaps my solution will work for you. When I opened an RStudio project, I found that if I called "library(here)", the root directory is set where the .Rproj file is located and that "set_here" would not change that directory, despite the 'here' package documentation. Perhaps I was doing something wrong, but I decided to solve the problem with a simple R function that moves up the directory tree until it finds a ".here" file. It then loads the "here" package and that sets the root directory where I want it.
I use "touch .here" in a Terminal outside of R to set my root directory, and then call "init_here()" from my newly opened R project:
init_here <- function() {
`%!in%` = Negate(`%in%`)
files <- dir( all.files = T )
while ( ".here" %!in% files & getwd()!="/" ) {
setwd("..")
files <- dir( all.files = T )
}
library(here)
}
Use Case -
In Unix:
cd( '~/myRoot' )
touch( '.here' )
In RStudio, when I open a project, the calls look like:
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
< R information removed for clarity >
[Workspace loaded from ~/myRoot/myProject/.RData]
> getwd()
[1] "/Users/me/myRoot/myProject"
> init_here()
here() starts at /Users/me/myRoot
> here()
[1] "/Users/me/myRoot"
>
I can now put a ".here" file at the root of each of my RStudio projects and set the expected root directory independently for each project. If you want to get fancy, you could put the function in each project's .Rprofile so that it runs whenever the project is opened. All of my projects have the .Rproj file in the directory above my "R" directory, so my .Rprofile looks like:
source("./R/init_here.R")
init_here()
Hope that helps.
Did you try simply adding a cd /the/path/where/you/put/the/files command in your shell script?
According to this documentation, here() "uses a reasonable heuristics to find your project's files, based on the current working directory at the time when the package is loaded". The "cd" (change directory) command in a shell script changes the current working directory.
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
I have a "copy deployed" installation of R with no R-specific environment variables set.
I want to source a file from within Rprofile.site:
source("how/to/find/this/file/my_settings.R")
Where could I place my my_settings.R file so that it can be found from within Rprofile.site no matter in which path Rprofile.site is installed?
BTW: I want to avoid an absolute path to my_settings.R this would work indeed. I'd prefer to use the same folder as Rprofile.site or a path relative to it to support copy deployment of R.
Edit 1: The problem is that getwd is always different depending on the current folder from which you start R
If you can't use absolute paths and that your working directory is not stable, one way is to use .libPaths or .Library.
By default your Rprofile should be in directory paste0(.Library,"/../etc/") or paste0(.libPaths()[2],"/etc/") so you can put your file there and source it with :
source(paste0(.Library,"/../etc/my_settings.R"))
source(paste0(.libPaths()[2],"/etc/my_settings.R"))
As far as I understand the first option is stable (I don't think one can change the value of .Library).
If you use the second option just make sure that if in the future you alter your .libPaths() you do it after sourcing your file.
See ?.libPaths for more info on default folders.
I want to change the prompt in R from > to R> and I know I should use the options command options(prompt="...") and it works, but then when I restart R the prompt is back to >.
Is there anyway to save the change so that it sticks?
Use .Rprofile file:
You can customize the R environment through a site initialization file or a directory initialization file. R will always source the Rprofile.site file first. On Windows, the file is in the C:\Program Files\R\R-n.n.n\etc directory. You can also place a .Rprofile file in any directory that you are going to run R from or in the user home directory.
At startup, R will source the Rprofile.site file. It will then look for a .Rprofile file to source in the current working directory. If it doesn't find it, it will look for one in the user's home directory. There are two special functions you can place in these files. .First( ) will be run at the start of the R session and .Last( ) will be run at the end of the session.
More details are here
I would like to know how I can set the pdflatex path in R to use sweave. Because I have 2 different MikTeX installations and one is working properly. Please take into account that I am using R (RStudio) in Windows. I found some suggestion however, for Linux or Unix users.
thanks in advance
If you have multiple installs of LaTeX (i.e. MikTeX) and you want to use a specific one of these, then you need to make sure that R finds the one you need first. This means that you have to add the location of your preferred version of pdfLaTeX at the front of your PATH system environment variable.
If you do not have administrator rights in Windows, then you can use R's environment file to change the PATH variable for R only. See ?Startup in R for details on this process. Follow the following steps:
in R, check the output of Sys.getenv("R_ENVIRON"). This will return the full path to an existing environment file, but will be empty in most cases. If a file exists, skip to step 3 below.
if no path is returned in step 1, create a file Renviron.site in the folder R_HOME/etc where R_HOME is the path returned by Sys.getenv("R_HOME").
add a line to the environment file as follows: PATH=C:\\full\\path\\to\\the\\folder\\with\\pdflatex;"${PATH}" (the quotations marks are important)
restart R and check Sys.getenv("PATH") and Sys.which("pdflatex") returns the correct paths.
If you do not have rights to create a Renviron.site file in R_HOME\etc, then you can also create a .Renviron file in HOME (Sys.getenv("HOME")).