Quit and restart a clean R session from within R? - r

Is there a way I can make an alias, within R, that will execute q() and then restart a clean R session?
And yes, I am too lazy to type q() and then the letter R :)

If you're in RStudio:
command/ctrl + shift + F10
You can also use
.rs.restartR()

Depending on how you start R try placing one of these lines into your .Rprofile file:
makeActiveBinding("refresh", function() { shell("Rgui"); q("no") }, .GlobalEnv)
makeActiveBinding("refresh", function() { system("R"); q("no") }, .GlobalEnv)
Then entering this into the R console:
refresh
will shut down the current session and start up a new one.

I found that .rs.restartR() works similar to pressing ctrl+shift+F10. but dose not unload the packages

As another alternative, Emacs ESS (>= 16.10) can reload the inferior R process via inferior-ess-r-reload-hook which is bound to C-c C-e C-r by default.

After looking for a solution to this, I solved my problem based on this solution here, using the R Package RDCOMClient.
The solution bellow just work within RStudio (Windows), once it simulates the keypresses ctrl+ shift + F10.
The RDCOMClient package must be installed with the command bellow:
install.packages("RDCOMClient", repos = "http://www.omegahat.net/R")
The code to simulate the keypresses within RStudio (Windows 10) are:
library(RDCOMClient)
wsh <- COMCreate("Wscript.Shell")
wsh$SendKeys("^+{F10}")
In the last line in the code above, the 'ctrl' key is represented by '^' and the shift key by '+'. All the explanations for this key representaions are available here.
Just after running the last line of the code above, the whole R session in RStudio will be reset, according to #steadyfish's comment. That is, it removes all the data from current session and unload all the loaded packages in the session.

Old post, but none of the answers quite work (for me, I'm using Windows, haven't tested others), so I'll add my solution. Some of my terminology might be off here, but this should get the point across:
Above answers don't quite work
Most of the answers submitted here involve using shell or system which doesn't quite work because while they open a new R console and do instruct the original console to close, the new console is a process running in the application context of the old console. That means the original console cannot close until the new console closes. Some of the users above such as hedgedandlevered reported that closing the original console forces the new console to close. When I try, the new console does open, but the old console remains open in a frozen state until the new console is closed.
The basic problem is calling shell or system does not change the application context from the original console to the new one, and therefore the original process cannot terminate until the new console closes.
Alternative that works for me
Instead use shell.exec which would normally be used to open a file in the default application based on file type. When used on a .exe, apparently, it runs the executable. The important difference, though, is that the system starts the application in it's own separate context. So here's the code that works for me:
makeActiveBinding("restart.R", function() { shell.exec(paste0(R.home(),"/bin/x64/Rgui.exe")); q("no") }, .GlobalEnv)
You'll need to edit the file path /bin/x64/Rgui.exe to match whatever you use to start R. You just put this line in your .Rprofile file, then you can call it by entering restart.R in your R code.
The downside of this over other methods is that you can't pass command line arguments like --no-save as you would with just shell, but at least this will let you close out the original R process.

Write this function in your .Rprofile
r <- function() {
assign('.Last', function() {system('R')}, envir = globalenv())
quit(save = 'no')
}
r() restarts you R session. Loaded packages will not reload. Your environment wont be saved.
Works for Linux. No idea of what may happen on other OS

In line with Martin Morgan's idea of using .Last(); this restarts R with the same set of command-line options as previously called:
restart_r <- function(status = 0, debug = TRUE) {
if (debug) message("restart_r(): Customizing .Last() to relaunch R ...")
assign(".Last", function() {
args <- commandArgs()
system2(args[1], args = args[-1])
}, envir = globalenv())
if (debug) message("restart_r(): Quitting current R session and starting a new one ...")
quit(save = "no", status = status, runLast = TRUE)
}

I needed the same refresh session functionality on windows and I ended up with a slightly modified version of the code:
makeActiveBinding("refresh", function() { shell(paste0("start \"\" \"", R.home(), "/bin/x64/Rgui.exe\"")); q("no") }, .GlobalEnv)
On windows you need to modify the Rprofile.site file. It is under R's etc directory. Also watch out for the last part of the path the bin/x64 can change according to your system configuration. I hope this will help others too.

I think, one realizes the best use of R by setting a current working directory in options. Then whenever your workspace /session file starts showing you up or has enough of your work in it (in between projects) you can just rename this default session file in the working directory after closing R and R/Rstudio will automatically start you in a new workspace/session file, without disturbing your current work.
Remember to quit R and rename the current session file
Of course if you do not want to save the current work you have to make sure you reset objects or operations on them were done after copying from original objects so they are as is. Trust me, knowing you can always load the old workspaces is a temptation but is more useful than not.
In short quit R, it gives you some gap while quitting means this workspace is full, rename it after completing the quit and restart R/Rstudio with a fresh workspace. You can always load select objects in the new workspace. Ideally all important work should be in Project directories but you still need a history of your jobs to go back to at times and saved sessions come in useful at some point once you are on longer projects. If you don't need any of it just rm(list=ls())
Also, I like the RDComClient idea by #Eduardo Alvin but it has been discontinued.
ALTERNATIVE OPTION
A simple alternative to get rid of the baggage at any time inside your workspace is to use save.image
save.image("Rstreamingscience.data")
quit(save='no')
load("Rstreamingscience.data") ##G:/ADA registers##
save.image("Rstreamingscience.data")
This leaves you free to come and go as you please and open as many workspaces as you need.

makeActiveBinding("refresh", function() { system(paste0(R.home(),"/bin/i386/R")); q("no") }, .GlobalEnv)
or with --save or --no-save
paste0(R.home(),"/bin/i386/R --no-save")
I think this is what you need if you've used setwd() before calling refresh (although neither this nor the original version works for me, since it restarts R then closes itself, a new window is never opened. If anyone can comment on this, please do so)

I have written the following function.
Remember! You can only use it once, then you have to reload it after the R session restarts.
clc <- function() {
rm(list = ls(envir = globalenv()),envir = globalenv()) #clear Vars from global enviroment
gc() #grabage colector
cat("\014") #clc
.rs.restartR() #clear session
}
Sometimes detaching a package also helps.

Related

.First() does not execute; win7 Rgui

With this in .Rprofile (first line copied from ?Startup examples):
.First <- function() cat("\n Welcome to R!\n\n")
foo <- "bar"
I do not see the Welcome text. The following shows that .Rprofile executes.
ls()
[1] "foo"
Apparently .First() does not execute. Any idea why not?
I'm running in an Rgui console on win7pro with R v3.6.1 x64.
I already learned that I will not be able to do what I wanted to do in .First(), but I still want to know why it is not even executing. I might want to use it for something in the future. I haven't made any fancy configuration changes, and I launch the console from a shortcut to Rgui.exe.
Solved: Early on I had bad code in .First(). While troubleshooting I cleared the workspace with
rm(list=ls())
q('yes')
That way the assignment foo<-"bar" more clearly showed that .Rprofile was executing. What I didn't realize was that the bad .First() got saved in some hidden environment in .RData. After that, no matter what I did with .First() in .Rprofile, it always got replaced with the bad one. To solve the problem, I just needed to delete .RData.
Update: .First() does not go into a hidden environment, but the starting dot makes it hide from ls(). To exit with a completely clear workspace, the code would be:
rm( list=ls(all.names=T) )
q('yes')
That's a lot of typing. In the future, I think I'll just delete .RData.
To me this seems a lot like a bug. Anytime you change .First() in .Rprofile, you need to delete .RData from every folder where you use R or execute rm(.First) and `q('yes') in every folder. That just begs for something to be missed.

Clear R environment of all objetcs & packages

I tried this command
remove(list = ls())
I expect to clear all R environment (Objects, packages)
The simplest and, more importantly, the only reliable way of doing this is to restart R. That takes care of everything.
Just make sure you’re not accidentally saving the current R image when quitting R.
In RStudio, you need to set the option “Save workspace to .RData file on exit” to “Never”, and disable restoring upon restart — this is strongly recommended!
After that, make sure that any previously existing .RData files in your project’s folder are deleted (heads up: .RData is an invisible file so you won’t normally see it in a file browser; you can delete it via the command line).
To restart R from within RStudio, you can use “Session” › “Restart R” or Cmd+Shift+F10.
The answer was already out there :-) https://stackoverflow.com/a/7506112/7902133
According to this answer, the following code should work
lapply(paste("package:", names(sessionInfo()$otherPkgs), sep=""),
detach,
character.only = TRUE,
unload = TRUE)
You may also want to check the first answer for a full description.
The freshr package has consolidated the previous answers into one simple function. Install it via
install.packages("freshr")
and then run
freshr::freshr()
in your console and it will unload all packages and variables for you.

Restart R within Rstudio

I'm trying to call a simple python script from within R using system2(). I've read some information I found vague that said if 'too much' memory is used, it won't work.
If I load a large dataset and use some information in it to use as arguments to pass into system2(), it will only work if I manually click "Restart R" in call Rstudio.
What I want:
df <- read.csv('some_large_file.csv')
###extracting some info called 'args_vec'
for(arg in args_vec){
system2('python', args)
}
This won't work as is. The for loop is simply passed over.
What I need:
df <- read.csv('some_large_file.csv')
###extracting some info called 'args_vec'
###something that 'restarts' R
for(arg in args_vec){
system2('python', args)
}
This answer doesn't quite get what I want. Namely, it doesn't work for me within Rstudio and it calls "system" (which presents the same problem as "system2" in this case). In fact, when I put the answer referenced above in my Rprofile.site file, it just immediately closed rstudio:
I tried the suggestion as a normal function (rather than using "makeActiveBinding", and it didn't quite work.
##restart R in r session -- doesn't work
makeActiveBinding("refresh", function() { system("R --save"); q("no") }, .GlobalEnv)
##nor did this:
refresh <- function() { system("R --save"); q("no") }
I tried a number of variations of these two options above, but this is getting long for what feels like a simple question. There's a lot I don't yet understand about the startup process and "makeActiveBinding" is a bit mysterious. Can anyone point me in the right direction?
In Rstudio, you can restart the R session by:
command/ctrl + shift + F10
You can also use:
.rs.restartR()
RStudio has this undocumented rs.restartR() which is supposed to do just that: restarting R.
However, it does not unload the packages that were loaded, nor does it clean the environment, so that I have some doubts about if it restarts R at all.
If you use RStudio, use the menu item Session > Restart R or the associated keyboard shortcut Ctrl+Shift+F10 (Windows and Linux) or Command+Shift+F10 (Mac OS). Additional keyboard shortcuts make it easy to restart development where you left off, i.e. to say “re-run all the code up to HERE”:
In an R script, use Ctrl+Alt+B (Windows and Linux) or Command+Option+B (Mac OS)
In R markdown, use Ctrl+Alt+P (Windows and Linux) or Command+Option+P (Mac OS)
If you run R from the shell, use Ctrl+D or q() to quit, then restart R.
Have you tried embedding the function call within the apply function, rather than a for loop?
I've had some pieces of code that ran the system out of memory in a for loop run perfectly with apply. It might help?
For those not limited to a command that want something that actually resets the system (no prior state, no loaded packages, no variables, etc.) you can select Terminate R from the Session menu.
It is a bit awkward (asks you if you are sure). If anyone knows something like clear all or really clear classes in MATLAB let me know!

Make a user-created function in R

I'm sorry if this has been asked before but I can't find the answer.
Let's say I write a small function in R
add2<-function(a){
return(a+2)
}
I save it as add2.R in my home directory (or any directory). How do I get R to find it??
> add2(4)
Error: could not find function "add2"
I know I can open up the script, copy/paste it in the console, run it, and then it works. But how do I get it built-in so if I open and close R, it still runs without me copying and pasting it in?
One lightweight option:
dump("add2", file="myFunction.R")
## Then in a subsequent R session
source("myFunction.R")
An alternative:
save("add2", file="myFunction.Rdata")
## Then just double click on "myFunction.Rdata" to open
## an R session with add2() already in it
## You can also import the function to any other R session with
load("myFunction.Rdata")
Until you're ready to package up functions into your own private package, storing them in well organized, source()-ready text files (as in the 1st example above) is probably the best strategy. See this highly up-voted SO question for some examples of how experienced useRs put this approach into practice.
Before invoking the function (e.g. at the beginning of the script), you should source the file containing your user defined function/s, i.e. :
source("add2.R") # this executes add2.R script loading add2 function
Basically, source function executes the code included in the script passed as argument. So if the file contains only functions definitions it loads the function in memory for future use.
If you want to start it automatically, then you have to set-up startup script and then use one of the methods outlined in answers above.
/Library/Frameworks/R.framework/Versions/2.15/Resources/etc/
is(for mac) the location of Rprofile.site, which must be edited adequately.
My version of it is:
.First <- function()
{
dir='~/Desktop/Infobase/R/0_init/0_init.R'
if(file.exists(dir))
{
source(dir, chdir = TRUE)
} else {cat("startup file is not found at:",dir)}
cat("\nWelcome at", date(), "\n")
}
.Last <- function()
{
cat("\nGoodbye at ", date(), "\n")
}
Note, that after you have sourced 1 R script, you do not need to enter this file anymore. Just do all you need from the file you sourced. In my case file "0_init.R" contains no functions, it just contains loading of other scripts. Well, you've got the idea.
Also, if you are doing this I recommend you to store them in new environment. Actual environments are not really suitable for your own functions(They are better implemented if you have a package developed, otherwise you lose a lot of control).
use "attach", "detach", "search", etc....
attach(FUN,name="af2tr")

Starting R and calling a script from a batch file

I have an R-based GUI that allows some non-technical users access to a stats model. As it stands, the users have to first load R and then type loadGui() at the command line.
While this isn't overly challenging, I don't like having to make non-technical people type anything at a command line. I had the idea of writing a .bat file (users are all running Windows, though multi-platform solutions also appreciated) that starts R GUI, then autoruns that command.
My first problem is opening RGui from the command line. While I can provide an explicit path, such as
"%ProgramW6432%\R\R-2.15.1\bin\i386\Rgui.exe"
it will need updating each time R is upgraded. It would be better to retrieve the location of RGui from the %path% environment variable, but I don't know an easy way to parse that.
The second, larger problem is how to call commands for R on startup from the command line. My first thought is that I could take a copy of ~/.Rprofile, append the extra command, and then replace the original copy of the file once R is loaded. This is awfully messy though, so I'd like an alternative.
Running R in batch mode isn't an option, firstly since I can't persuade GUIs to display themselves, and secondly because I would like the R console available, even if the users shouldn't need to use it.
If you want a toy GUI to test your ideas, try this:
loadGui <- function()
{
library(gWidgetstclck)
win <- gwindow("test")
rad <- gradio(letters[1:3], cont = win)
}
Problem 1: I simply do not ever install in the suggested default directory on Windows, but rather group R and a few related things in, say, c:/opt/ where I install R itself in, say,c:/opt/R-current so that the path c:/opt/R-current/bin will remain constant. On upgrade, I first renamed to R-previous and then install into a new R-current.
Problem 2: I think I solved that many moons ago with scripts. You can now use Rscript.exe to launch these, and there are tcltk examples for waiting for a prompt.
I have done similar a couple of times. In my cases the client was using windows so I just installed R on their computer and created a shortcut on their desktop to run R. Then I right click on the shortcut and choose properties to get the propertiest dialog. I then changed the "Start in" folder to the one where I wanted it to run from (which had the .Rdata file with the correct data and either a .First function in the .Rdata file or .Rprofile in the folder). There is also a "Run:" option that has a "Minimized" option to run the main R window minimized.
I had created the functions that I wanted to run (usually a specialized gui using tcltk) and any needed data and saved them in the .Rdata file and also either created .First or .Rprofile to run the comnand that showed the gui. The user double clicks on the icon on the desktop and up pops my GUI that they can work with while ignoring the other parts.
Take a look at the ProjectTemplate library. It does what you want to do. It loads used libraries from a batch file an run R files automatically after loading as well as a lot of other usefull stuff as well...
Using the answer from https://stackoverflow.com/a/27350487/41338 and a comment from Richie Cotton above I have arrived at the following solution to keeping a script alive until a window is closed by checking if the pointer to the window is valid.
For a RGtk2 window created and shown using:
library(RGtk2)
mainWindow <- gtkWindow("toplevel", show = TRUE)
Create a function which checks if the pointer to it exists:
isnull <- function(pointer){
a <- attributes(pointer)
attributes(pointer) <- NULL
out <- identical(pointer, new("externalptr"))
attributes(pointer) <- a
return(out)
}
and at the end of your script:
while(!isnull(mainWindow)) Sys.sleep(1)

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