So I tried adding R to the path on windows 10 (that is supposedly easy).
System Properties -> Environment variables -> Edit -> new: copy and paste: "C:\Program Files\R\R-3.5.0\bin\x64"
Now the thing is, Powershell just refuses to start the R environment when I type in R. R.exe works apparently. Rgui works as well. Is R a reserved letter in powershell or something? It also seems to repeat the previous command sometimes but that doesn't really seem completely consistent either.
(I put this entry on top of the list of the path and restarted the pc already)
when entering get-alias r I got the following result, so yes "r" is already taken ...
CommandType Name Version Source
----------- ---- ------- ------
Alias r -> Invoke-History
PS: you could remove that alias with remove-item alias:\r from your current powershell session and test if "r" then starts "R.exe". if that works for you, you could edit your profile to remove the alias "r -> Invoke-History" from every new session.
To generalize Guenther Schmitz' helpful answer:
PowerShell has several types of commands, whose precedence is:
Alias
Function
Cmdlet
External application
Note that name resolution is always case-insensitive, so that both r and R refer to the same command.
That is, before R resolves to R.exe, it is not only an r alias that could get in the way, but potentially also a function or a cmdlet (though the latter case is hypothetical, because well-behaved cmdlets follow a <Verb>-<Noun> naming pattern).
Note that built-in aliases shadowing external programs, especially standard ones, is problematic, and in the context of PowerShell Core a discussion is underway about whether to remove all built-in aliases and make them opt-in only - see this GitHub issue.
To see what a given name resolves to, use the Get-Command cmdlet:
# See what R resolves to
Get-Command R
# See ALL commands that R *can* resolve to, with the EFFECTIVE one listed first:
Get-Command -All R
Choices for unambiguously targeting R.exe:
(As you already know) If its folder is in one of the folders listed in environment variable $env:PATH, append .exe - i.e., use the filename extension explicitly:
R.exe ...
Use R.exe's full path (note the need for & for invocation, because the path needs quoting):
& "C:\Program Files\R\R-3.5.0\bin\x64\R.exe" ...
(For the sake of completeness; this is the cumbersome equivalent of using just R.exe): Use Get-Command -Type Application to locate the executable:
& (Get-Command -Type Application R) ...
Alternatively, as stated in Guenther's answer, you could add Remove-Alias r to your PowerShell $PROFILE file in order to remove the built-in alias on session startup, which then allows you to just use r to start R.exe.
Run the following code in your console to install the R package. This code will automatically add R to your os PATH.
sudo apt-get install littler
Related
The Julia Pkg documentation tells how to initiate an environment ($ activate $ENV-NAME), but it probably lacks the handy command to switch to the already created special environment. Also, I'm having trouble finding a command that shows all already created environments on the list, hence, if I have forgotten the names of the environments previously created, I need to do a manual search through the Julia-related folders...
So far, the verbatim help command in Julia REPL provides a poor description and so does the related Pkg-documentation webpage.
Another possible general answer to this predicament is to start using the Playground.jl module, which was recommended here on Medium:
However, the direct download attempt with Pkg repeatedly fails since the Pkg isn't able to find the package in the suggested GH project.
Thanks beforehand for any recommendations.
In package manager prompt just type activate # and press tab-key. The REPLs autocomplete will show you the possible environments.
If you are on a Mac or Linux
you can run this shell command to find all the "enviroment"
bash-3.2$ pwd
/Users/ssiew/juliascript
bash-3.2$ find . -name Project.toml
./Luxordir/Project.toml
./symata/Project.toml
After having set the path for the default working directory as well as my first (and only) project within RStudio options I wonder why RStudio keeps creating an empty folder named "R" within my "/home" directory every time it is started.
Is there any file I could delete/edit (eventually create) to stop this annoying behaviour and if so, where is it located ?
System: Linux Mint v. 19.3
Software: RStudio v. 1.3.959 / R version 3.4.4
Thanks in advance for any hints.
Yes, you can prevent the creation of the R directory — R is configurable via a set of environment variables.
However, setting these correctly isn’t trivial. The first issue is that many R packages are sensitive to the R version they’re installed with. If you upgrade R and try to load the existing package, it may break. Therefore, the R package library path should be specific to the R version.
On clusters, an additional issue is that the same library path might be read by various cluster nodes that run on different architectures; this is rare, but it happens. In such cases, compiled R packages might need to be different depending on the architecture.
Consequently, in general the R library path needs to be specific both to the R version and the system architecture.
Next, even if you configure an alternative path R will silently ignore it if it doesn’t exist. So be sure to manually create the directory that you’ve configured.
Lastly, where to put this configuration? One option would be to put it into the user environment file, the path of which can be specified with the environment variable R_ENVIRON_USER — it defaults to $HOME/.Renviron. This isn’t ideal though, because it means the user can’t temporarily override this setting when calling R: variables in this file override the calling environment.
Instead, I recommend setting this in the user profile (e.g. $HOME/.profile). However, when you use a desktop launcher to launch your RStudio, this file won’t be read, so be sure to edit your *.desktop file accordingly.1
So in sum, add the following to your $HOME/.profile:
export R_LIBS_USER=${XDG_DATA_HOME:-$HOME/.local/share}/R/%p-library/%v
And make sure this directory exists: re-source ~/.profile (launching a new shell inside the current one is not enough), and execute
mkdir -p "$(Rscript -e 'cat(Sys.getenv("R_LIBS_USER"))')"
The above is using the XDG base dir specification, which is the de-facto standard on Linux systems.2 The path is using the placeholders %p and %v. R will fill these in with the system platform and the R version (in the form major.minor), respectively.
If you want to use a custom R configuration file (“user profile”) and/or R environment file, I suggest setting their location in the same way, by configuring R_PROFILE_USER and R_ENVIRON_USER (since their default location, once again, is in the user home directory):
export R_PROFILE_USER=${XDG_CONFIG_HOME:-$HOME/.config}/R/rprofile
export R_ENVIRON_USER=${XDG_CONFIG_HOME:-$HOME/.config}/R/renviron
1 I don’t have a Linux desktop system but I believe that editing the Env entry to the following should do it:
Exec=env R_LIBS_USER=${XDG_DATA_HOME:-$HOME/.local/share}/R/%p-library/%v /path/to/rstudio
2 Other systems require different handling. On macOS, the canonical setting for the library location would be $HOME/Library/Application Support/R/library/%v. However, setting environment variables on macOS for GUI applications is frustratingly complicated.
On Windows, the canonical location is %LOCALAPPDATA%/R/library/%v. To set this variable, use [Environment]::SetEnvironmentVariable in PowerShell or, when using cmd.exe, use setx.
I tried to run a Python script from R with:
system('python script.py arg1 arg2')
And got an error:
ImportError: No module named pandas
This was a bit of a surprise since the script was working from the terminal as expected. Having encountered this type of issue before (with knitr, whence the engine.path chunk option), I know to check:
Sys.which('python')
# python
# "/usr/bin/python"
And compare it to the command line:
$ which python
# /Users/michael.chirico/anaconda2/bin/python
(i.e., the error arises because I have pandas installed for the anaconda distribution, though TBH I don't know why I have a different distribution)
Hence I can fix my issue by running:
system('/Users/michael.chirico/anaconda2/bin/python script.py arg1 arg2')
My question is two-fold:
How does R's system/Sys.which find a different python than my terminal?
How can I fix this besides writing out the full binary path each time?
I read ?Sys.which for some hints, but to no avail. In particular, ?Sys.which suggests Sys.which is using which:
This is an interface to the system command which
This is clearly (?) untrue; to be sure, I checked Sys.which('which') and which which to confirm both are pointing to /usr/bin/which (goaded on by this tidbit):
On a Unix-alike the full path to which (usually /usr/bin/which) is found when R is installed.
To the latter, on a whim I tried Sys.setenv(python = '/Users/michael.chirico/anaconda2/bin/python') to no avail.
As some of the comments hint, this is a problem that arises because the PATH environment variable is different for programs launched by Finder (or the Dock) than it is in the Terminal. There are ways to set the PATH for Dock-launched applications, but they aren't pretty. Here's a place to start looking if you want to go that route:
https://apple.stackexchange.com/questions/51677/how-to-set-path-for-finder-launched-applications
The other thing you can do, which is probably more straightforward, is tell R to set the PATH variable when it starts up, using Sys.setenv to add the path to your desired Python instance. You can do that for just one project, for your whole user account, or for the whole system, by placing the command in a .Rprofile file in the corresponding location. More information on how to do this here:
https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
How does R's built-in system() function know where to look to invoke some arbitrary OS command specified by the command argument? For example, if I homebrew install some_command_line_program, how does R's system() function know where it is located when I type:
cmd <- "some_complicated_code_from_some_command_line_program"
system(cmd, wait=FALSE)
In other words, how is R smart enough to know where to look without any user input? If I compile from source via Github (instead of homebrew install), would system() also recognize the command?
What system does depends on your OS, you've not told us (although you've given us some clues...).
On unix-alike systems, it executes it as a command in a bash shell, which searches for the first match in the directories on the $PATH environment variable. You can see what that is in R:
> Sys.getenv("PATH")
[1] "/usr/local/heroku/bin:/usr/local/heroku/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/nobackup/rowlings/NEST4B"
In Windows, it does something else.
You can get a full path to whatever it might run with Sys.which, which uses the systems' which command on unixes and fakes it on Windows. Read the help for more.
If you compile something from source then it will be found if the file that runs the command (a shell script, an executable, a #!-script in any language) is placed in a folder in your $PATH. You can create a folder yourself, say /home/user/bin, put your executables in there, add that to your $PATH, and (possibly after logging out an in again, or restarting R, or just firing up a new shell...) then R will find it.
Hello this is likely to be a silly question, sorry for that.
I want to change the library folder in Windows but I do not understand what is said in the cran website:
You may also want to add command-line arguments at the end of the Target field (after any final double quote, and separated by a space), for example --sdi --max-mem-size=1G. You can also set environment variables at the end of the Target field, for example R_LIBS=p:/myRlib, and if you want to ensure that menus and messages are in (American) English, LANGUAGE=en.
When I set the R_LIBS variable in R with R_LIBS="C:/R/i686-pc-linux-gnu-library/3.0" it doen't give any error but the folder path for the library does not change becuse when I type require(package) it is not found.
I saw this post and it says it can be due to the R.profile. I don't know how to deal with the error, should I just remove R and install it from the beginning?
You should set the environment variable R_LIBS in Windows ( not within R) to something like
R_LIBS=C:/R/i686-pc-linux-gnu-library/3.0
Restart R.
Note to set the environment variable you can use setx command:
Open a cmd console (command line console)
setx R_LIBS %R_LIBS%;C:/R/i686-pc-linux-gnu-library/3.0;