A combination of frustrating problems here. Essentially I want R to open an external program with command line parameters. I am currently trying to achieve it on a Windows machine, ideally it would work cross-platform.
The program (chimera.exe) is in a directory containing spaces: C:\Program Files\Chimera1.15\bin\
The command line options could be for instance a --nogui flag and a script name, so from the shell I would write (space-specifics aside):
C:\Program Files\Chimera1.15\bin\chimera.exe --nogui scriptfile
This works if I go in windows cmd.exe to the directory itself and just type chimera.exe --nogui scriptfile
Now in R:
I've been playing with shell(), shell.exec(), and system(), but essentially I fail because of the spaces and/or the path separators.
most of the times system() just prints "127" for whatever reason:
> system("C:/Program Files/Chimera1.15/bin/chimera.exe")
[1] 127`
back/forward slashes complicate the matter further but don't make it work:
> system("C:\Program Files\Chimera1.15\bin\chimera.exe")
Error: '\P' is an unrecognized escape in character string starting "C\P"
> system("C:\\Program Files\\Chimera1.15\\bin\\chimera.exe")
[1] 127
> system("C:\\Program\ Files\\Chimera1.15\\bin\\chimera.exe")
[1] 127
> system("C:\\Program\\ Files\\Chimera1.15\\bin\\chimera.exe")
[1] 127
When I install the program in a directory without spaces, it works. How can I escape or pass on the space in system() or related commands or how do I invoke the program otherwise?
Try system2 as it does not use the cmd line processor and use r"{...}" to avoid having to double backslashes. This assumes R 4.0 or later. See ?Quotes for the full definition of the quotes syntax.
chimera <- r"{C:\Program Files\Chimera1.15\bin\chimera.exe}"
system2(chimera, c("--nogui", "myscript"))
For example, this works for me (you might need to change the path):
R <- r"{C:\Program Files\R\R-4.1\bin\x64\Rgui.exe}" # modify as needed
system2(R, c("abc", "def"))
and when Rgui is launched we can verify that the arguments were passed by running this in the new instance of R:
commandArgs()
## [1] "C:\\PROGRA~1\\R\\R-4.1\\bin\\x64\\Rgui.exe"
## [2] "abc"
## [3] "def"
Alternately use system but put quotes around the path so that cmd interprets it correctly -- if it were typed into the Windows cmd line the quotes would be needed too.
system(r"{"C:\Program Files\Chimera1.15\bin\chimera.exe" --nogui myscript}")