I am using RStudio and at times I want to remove some files in the working directory (e.g., previously generated .csv files).
It is quite inconvenient to frequently switch to bash and execute rm. Is there any way of invoking commands in the R console?
See here
Use system (or shell) as agstudy's comment says
e.g. system("pwd")
If you are just removing files, rather than executing arbitrary commands on the shell, you would be better off following Thomas's suggestion:
?file.remove
Using this function instead of shell("rm example.csv") is safer and more portable.
Related
Is it possible to determine - from within the script - whether the script is running in the R-GUI (specifically R.app on OS X) or whether it has been called from Terminal/command line (i.e. R --vanilla -f script.R)? If so, how is this possible?
I'm asking because I have a script that can run parallelized (using the doMC library), which should not be used from the GUI. Sometimes I need to further process the data calculated in the script, so I'd like to call the script from the GUI on these occasions.
Perhaps you are looking for interactive()?
In C, you would use the isatty function. If you could find an equivalent function in R (probably in a UNIX or file system library), that should help.
Current script
I work on Mac OSX. I have an R script that I like to use to organize my files and produce .pdf via LaTex. In order to (1) produce the .pdf with LaTeX and (2) manipulate some files and directories I use Bash script from R with system("").
From Mac to Windows
I would like to offer this R script (once compiled to make an executable) to someone that knows nothing about programming and uses Windows. I have no idea how the windows prompt commands work and what language it uses. I am afraid that (1) I cannot use the function system("") on Windows and (2) I cannot use bash such as system("rm dir/file.txt").
Question
What do you think would be the easiest for me in order to make my script compatible with Windows (given that I know nothing about Windows)? Will I be able to use system("") and Bash from R on Windows?
I think the best solution is to handle both cases separately (keep in mind that windows paths are also different from unix paths).
if(.Platform$OS.type == "unix") {
system("rm dir/file.txt")
[...]
}
else {
system("DEL /Q dir\file.txt")
[...]
}
You should have no problem searching for unix equivalent commands in windows cmd.
Also keep in mind that if you need the R script to exec LaTeX binaries, it would pretty much kill the portability because of the huge dependencies that LaTeX has.
Hej,
When I try to call QIIME with a system call from R, i.e
system2("macqiime")
R stops responding. It's no problem with other command line programs though.
can certain programs not be called from R via system2() ?
MacQIIME version:
MacQIIME 1.8.0-20140103
Sourcing MacQIIME environment variables...
This is the same as a normal terminal shell, except your default
python is DIFFERENT (/macqiime/bin/python) and there are other new
QIIME-related things in your PATH.
(note that I am primarily interested to call QIIME from R Markdown with engine = "sh" which fails, too. But I strongly suspect the problems are related)
In my experience, when you call Qiime from unix command line, it usually creates a virtual shell of it`s own to run its commands which is different from regular system commands like ls or mv. I suspect you may not be able to run Qiime from within R unless you emulate that same shell or configuration Qiime requires. I tried to run it from a python script and was not successful.
I'm trying to use a Windows computer to SSH into a Mac server, run a program, and transfer the output data back to my Windows. I've been able to successfully do this manually using Putty.
Now, I'm attempting to automate the process using Plink. I've added Plink to my Windows Path, so if I open cmd and type in a command, I can successfully log in and pass commands to the server:
However, I'd like to automate this using R, to streamline the data analysis process. Based on some searching, the internet seems to think that the shell command is best suited to this task. Unfortunately, it doesn't seem to find Plink, though passing commands through shell to the terminal is working:
If I try the same thing but manually setting the path to Plink using shell, no output is returned, but the commands do not seem to run (e.g. TESTFOLDER is not created):
Does anyone have any ideas for why Plink is unavailable when I try to call it from R? Alternately, if there are other ideas for how this could be accomplished in R, that would also be appreciated.
Thanks in advance,
-sam
I came here looking for an answer to this question, so I only have so much to offer, but I think I managed to get PLINK's initial steps to work in R using the shell function...
This is what worked for me:
NOT in R:
Install PLINK and add its location to your PATH.
Download the example files from PLINK's tutorial (http://pngu.mgh.harvard.edu/~purcell/plink/tutorial.shtml) and put them in a folder whose path contains NO spaces (unless you know something I don't, in which case, space it up).
Then, in R:
## Set your working directory as the path to the PLINK program files: ##
setwd("C:/Program Files/plink-1.07-dos")
## Use shell to check that you are now in the right directory: ##
shell("cd")
## At this point, the command "plink" should be at least be recognized
# (though you may get a different error)
shell("plink")
## Open the PLINK example files ##
# FYI mine are in "C:/PLINK/", so replace that accordingly...
shell("plink --file C:\\PLINK\\hapmap1")
## Make a binary PED file ##
# (provide the full path, not just the file name)
shell("plink --file C:\\PLINK\\hapmap1 --make-bed --out C:\\PLINK\\hapmap1")
... and so on.
That's all I've done so far. But with any luck, mirroring the structure and general format of those lines of code should allow you to do what you like with PLINK from within R.
Hope that helps!
PS. The PLINK output should just print in your R console when you run the lines above.
All the best,
- CC.
Just saw Caitlin's response and it reminded me I hadn't ever updated with my solution. My approach was kind of a workaround, rather than solving my specific problem, but it may be useful to others.
After adding Plink to my PATH, I created a batch script in Windows which contained all my Plink commands, then called the batch script from R using the command shell:
So, in R:
shell('BatchScript.bat')
The batch script contained all my commands that I wanted to use in Plink:
:: transfer file to phosphorus
pscp C:\Users\Sam\...\file zipper#144.**.**.208:/home/zipper/
:: open connection to Dolphin using plink
plink -ssh zipper#144.**.**.208 Batch_Script_With_Remote_Machine_Commands.bat
:: transfer output back to local machine
pscp zipper#144.**.**.208:/home/zipper/output/ C:\Users\Sam\..\output\
Hope that helps someone!
I have created a batch file to launch R scripts in Rterm.exe. This works well for regular weekly tasks. The < PBWeeklyMeetingScriptV3.R > is the R script run by Rterm.
set R_TERM="C:\Program Files\R\R-2.14.0\bin\x64\Rterm.exe"
%R_TERM% --slave --no-restore --no-save --args 20120401 20110403 01-apr-12 03-apr-11 < PBWeeklyMeetingScriptV3.R > PBWeeklyMeetingScriptV3.batch 2> error.txt
I've tried to modify this to launch the R GUI instead of the background process as I'd like to inspect and potentially manipulate and inspect the data.
If I change my batch file to:
set R_TERM="C:\Program Files\R\R-2.14.0\bin\x64\Rgui.exe"
the batch file will launch the R GUI but doesn't start the script. Is there a way to launch the script too?
Alternatively is there a way to save/load the work space image to access the variables that are created in the script?
You can save and load workspaces by using save.image() and load(). I do this all the time when scripting to pass data sets between two separate script files, tied together using Python or bash. At the end of each R script, just add:
save.image("Your_image_name.RData")
The image will be the workspace that existed whenever the command was run (so, if it's the last command in the file, it's the workspace right before the exist of the file). We also use this at my job to create "snapshots" of input and output data, so we can reproduce the research later. (We use a simple naming convention to get the time of run, and then label the files with that).
Not sure about launching and then running the GUI with specific scripts in it; I don't think that's a feature you'll find in R, simply because the whole point of running a batch file is usually to avoid the GUI. But hopefully, you can just save the image to disk, and then look at it or pass it to other programs as needed. Hope that helps!