After seven hours of googling and rereading through somewhat similar questions, and then lots of trial and error, I'm now comfortable asking for some guidance.
To simplify my actual task, I created a very basic R script (named test_script):
x <- c(1,2,3,4,5)
avg <- mean(x)
write.csv(avg, file = "output.csv")
This works as expected.
I'm new to python and I'm just trying to figure out how to execute the R script so that the same .csv file is created.
Notable results come from:
subprocess.call(["C:/Program Files/R/R-2.15.2/bin/R", 'C:/Users/matt/Desktop/test_script.R'])
This opens a cmd window with the typical R start-up verbiage, except there is a message which reads, "ARGUMENT 'C:/Users/matt/Desktop/test_script.R' __ ignored __"
And:
subprocess.call(['C:/Program Files/R/R-2.15.2/bin/Rscript', 'C:/Users/matt/Desktop/test_script.r'])
This flashes a cmd window and returns a 0, but no .csv file is created.
Otherwise, I've tried every suggestion I could identify on this site or any other. Any insight will be greatly appreciated. Thanks in advance for your time and efforts.
Running R --help at the command prompt prints:
Usage: R [options] [< infile] [> outfile]
or: R CMD command [arguments]
Start R, a system for statistical computation and graphics, with the
specified options, or invoke an R tool via the 'R CMD' interface.
Options:
-h, --help Print short help message and exit
--version Print version info and exit
...
-f FILE, --file=FILE Take input from 'FILE'
-e EXPR Execute 'EXPR' and exit
FILE may contain spaces but not shell metacharacers.
Commands:
BATCH Run R in batch mode
COMPILE Compile files for use with R
...
Try
call(["C:/Program Files/R/R-2.15.2/bin/R", '-f', 'C:/Users/matt/Desktop/test_script.R'])
There are also some other command-line arguments you can pass to R that may be helpful. Run R --help to see the full list.
It might be too late, but hope it helps for others:
Just add --vanilla in the call list.
subprocess.call(['C:/Program Files/R/R-2.15.2/bin/Rscript', '--vanilla', 'C:/Users/matt/Desktop/test_script.r'])
Related
tl;dr: How can I invoke the system command y | conda create --name gee_interface from an R console, e.g. via system2()? I'm comfortable enough with system2('conda', c('create', '--name', 'gee_interface')), but I don't know how to handle piping in the 'y' via system2().
Details
I am trying to use an R console to run the bash command conda create --name gee_interface (OSX Mojave with Anaconda installed).
In terminal, that command executes just fine, but prompts me to answer with Proceed ([y]/n)? (I answer 'y' and everything works smoothly).
In R, I run
Sys.setenv(PATH = paste(c("/Applications/anaconda3/bin", Sys.getenv("PATH")), collapse = .Platform$path.sep)) # ensures that system2() finds conda
system2('conda', c('create', '--name', 'gee_interface')) # This is the key line for the purposes of this question
When running the second line [i.e. system2('conda', c('create', '--name', 'gee_interface'))], the process never finishes, but quickly falls to zero CPU usage. Presumably the system is waiting for my response to the prompt, but I don't know how to provide it. How does one do this via an R script? Note also that in my particular case, the number of times that I need to respond 'y' is variable, depending on whether an environment of the name gee_interface already exists or not.
The fix to your first problem is to tell conda not to ask for confirmation using -y:
system2('conda', c('create', '--name', 'gee_interface', '-y'))
As to the second part (variable times that your input is required), I'm guessing it's to overwrite the environment if it exists? In that case, you could check for its existence first with conda info --envs, and run conda remove --name gee_interface --all if necessary before creating it.
See:
https://docs.conda.io/projects/conda/en/latest/commands/create.html
https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#removing-an-environment
You could also try your system2 call, with the argument input = "y", but that doesn't fix your second problem of needing to affirm multiple times.
See: Invoke a system command and pipe a variable as an argument
Sorry for a basic question. I'm trying run a R script called cuffdiff_gtf_attributes (please find it at enter link description here in R 3.3.1 installed on the Windows 7. The script is started with the below line:
#!/usr/bin/env Rscript
When I type cuffdiff_gtf_attributes in R, it says Error: object 'cuffdiff_gtf_attributes' not found. Also, I tried Rscript cuffdiff_gtf_attributes that returned me: Error: unexpected symbol in "Rscript cuffdiff_gtf_attributes".
Moreover, I tried source('cuffdiff_gtf_attributes.R')that seems to work and returned the usage of the script as bellow
Error:
usage: cuffdiff_gtf_attributes --input=<inputGTF> [--output=outputGTF] | --help
But, when I add the arguments as source('cuffdiff_gtf_attributes.R') --input=file.gtf, it says that: Error: object 'file.gtf' not found. I also tried this command as source('cuffdiff_gtf_attributes.R') --input file.gtf, it says that Error: unexpected symbol in "source('cuffdiff_gtf_attributes.R') --input file.gtf"
Sorry, I couldn't post a sample GTF file, you can find a short sample of it at enter link description here
Everything is the current path. Could you please help me out to execute the script?
Thanks in advance
This is a script file. You should run using Rscript instead for Rgui.exe. From a command prompt, navigate to the directory where file.gtf is and run:
"%Programfiles%\R\R-3.3.3\bin\Rscript" cuffdiff_gtf_attributes.R --input=file.gtf
I need to execute an external tool from R and process errors (if any) occurred in that tool.
I know 3 functions to do something familiar with my task:
shell, system and system2.
Trying to test those, I see that command
shell("notepad")
opens notepad. As far as I know shell doesn't allow to check errors (there's no interface to look into stderr).
When I call
system("notepad")
or
system2("notepad")
R freezes trying to make those commands.
Calling
system("start notepad")
or
system2("start notepad")
returns warning
Warning message:
running command '"start notepad"' had status 127
Adapting #DavidTseng's answer (sorry for not having enough reputation to upvote it)...
system("cmd.exe", input = "notepad")
worked for me in Windows.
As I mentioned in my comments, the R documentation reveals that in Windows the system() function does not launch a separate shell (if needed). This is why command line commands run with system(), but Notepad, which needs a separate window, does not run:
From the documentation for system():
The most important difference is that on a Unix-alike system launches a shell which then runs command. On Windows the command is run directly – use shell for an interface which runs command via a shell (by default the Windows shell cmd.exe, which has many differences from a POSIX shell).
system("bash -l", input = "notepad")
I'm not sure if there's been an update to R that allows this since the question was asked nearly four years ago, but system("\"C:\path\to\exe.exe\" args", intern = T) works for me and WILL bring up a separate child window and works on Windows 10 + R 3.6 + RStudio.
Not using the 'intern = T' was giving me a return code of 127 and did not run the process.
I had the same issue. there is an additional step in the installation process which i did not do.
refer to to the url
https://cran.r-project.org/bin/windows/Rtools/
Look for "Putting Rtools on the PATH"
writeLines('PATH="${RTOOLS40_HOME}\usr\bin;${PATH}"', con = "~/.Renviron")
for windows users
wrong: system(path("c:", "program files", "r", "anysoft.EXE"))
but works : system(path("c:", shQuote("program files"), "r", "anysoft.EXE"))
You guys are making it so complicated. I solved this problem by referring to this answer. The problem is with the PATH. type Sys.which('') in R, and you will see nothing. So you have to set the path in CMD, and then use Sys.setenv(PATH = '') in R to get this work.
I am new to programming and mainly I am able to do some scripts within R, but for my work I need to call an external program. For this program to work on the ubuntu's terminal I have to first use setenv and then execute the program. Googling I've found the system () and Sys.setenv() functions, but unfortunately I can make it function.
This is the code that does work in the ubuntu terminal:
$ export PATH=/home/meme/bin:$PATH
$ mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp
Where the first two arguments are input files, the -o argument is the output directory and the -comp is another parameter for the program to run.
The reason that I need to do it in R despite it already works in the terminal is because I need to run the program 1000 times with 1000 different files so I want to make a for loop where the input name changes in every loop and then analyze every output in R.
I have already tried to use:
Sys.setenv(PATH="/home/meme/bin"); system(mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp )
and
system(Sys.setenv(PATH="/home/meme/bin") && mast "/home/meme/meme.txt" "/home/meme/seqs.txt" -o "/home/meme/output" -comp )
but always received:
Error: unexpected constant string in "system(mast "/home/meme/meme.txt""
or
Error: unexpected symbol in "system(Sys.setenv(PATH="/home/meme/bin") && mast "/home/meme/meme.txt""
At this point I have run out of ideas to make this work. If this has already been answered, then my googling have just been poor and I would appreciate any links to its response.
Thank you very much for your time.
Carlos
Additional details:
I use Ubuntu 12.04 64-bits version, RStudio version 0.97.551, R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Platform: x86_64-pc-linux-gnu (64-bit).
The program I use (MAST) finds a sequence pattern in a list of letters and is part of the MEME SUIT version 4.9.1 found in http://meme.nbcr.net/meme/doc/meme-install.html and run through command line. The command-line usage for mast is:
mast <motif file> <sequence file> [options]
Construct the string you want to execute with paste and feed that to system:
for(i in 1:10){
cmd=paste("export FOO=",i," ; echo \"$FOO\" ",sep='')
system(cmd)
}
Note the use of sep='' to stop paste putting spaces in, and back-quoting quote marks in the string to preserve them.
Test before running by using print(cmd) instead of system(cmd) to make sure you are getting the right command built. Maybe do:
if(TESTING){print(cmd)}else{system(cmd)}
and set TESTING=TRUE or FALSE in R before running.
If you are going to be running more than one shell command per system call, it might be better to put them all in one shell script file and call that instead, passing parameters from R. Something like:
cmd = paste("/home/me/bin/dojob.sh ",i,i+1)
system(cmd)
and then dojob.sh is a shell script that parses the args. You'll need to learn a bit more shell scripting.
Is there a way to write my R errors to a file? I run R on bash via:
R --vanilla < myprogram > myprogram.out &
When my program encounters an error (not a syntax error...like an illegal replacement or something) it stops but the error line isn't written to the output file and I don't know what the program was and a lot of the time I log out from the server while it runs.
Thanks,
Josh
Use the R CMD BATCH <infile> <outfile> syntax instead.