I am attempting to call a system command from within an R script. The system command I want to call is a name of a software that I load as a module on a shared computing cluster (using singularity). The problem I am having is that the software is not able to run when I use the system command.
system_trial.R) has only one line:
system('STAR')
hostname[1] Rscript system_trial.R
sh: STAR: command not found
Warning message:
In system("STAR") : error in running command
Of course, the software works if I call it from the shell directly.
hostname[2] STAR
Usage: STAR [options]... --genomeDir /path/to/genome/index/ --readFilesIn R1.fq R2.fq
Spliced Transcripts Alignment to a Reference (c) Alexander Dobin, 2009-2020
If I run which STAR, I get singularity exec /apps/singularity-3/star/star-2.7.5a--0.sif STAR $#
Replacing system('STAR') with system('singularity exec /apps/singularity-3/star/star-2.7.5a--0.sif STAR $#') actually executes the software.
Replacing system('STAR') with system('which STAR'), returns which: no STAR in (/bin:etc...)
Using system2('STAR') gives sh: STAR: command not found.
I would like to simply use system('STAR'). How can I achieve this?
Related post without an answer: R: calling a system command
Related
I need to restart an R session running in linux using a line of code. When the R session restarts I need it to load an existing R script and for the new R session to be clear of previously loaded packages, variables etc.
I've managed to make this work from within an R terminal in Windows using the following code:
library(startup)
restart(args = c('source("existing_code.R")'))
However when the same code runs in a Linux environment I get the following error:
sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `'/opt/R/3.6.3/lib/R/bin/exec/R' source("
existing_code.R")'
I have a '.js' script that I usually activate from the terminal using the command node script.js. As this is part of a process where I first do some data analysis in R, I want to avoid the manual step of opening the terminal and typing the command by simply having R do it for me. My goal would be something like this:
...R analysis
write.csv(df, "data.csv")
system('node script.js')
However, when I use that specific code, I get the error:
sh: 1: node: not found
Warning message:
In system("node script.js") : error in running command
Of course, the same command runs without problem if I type it directly on the terminal.
About my Software
I am using:
Linux computer with the PopOS!
RStudio 2021.09.1+372 "Ghost Orchid"
R version 4.0.4.
The error message node: not found indicates that it couldn't find the program node. It's likely in PATH in your terminal's shell, but not in system()'s shell (sh).
In your terminal, locate node by executing which node. This will show the full path to the executable. Use that full path in system() instead.
Alternatively, run echo $PATH in your terminal, and run system('echo $PATH') or Sys.getenv('PATH') in R. Add any missing directories to R's path with Sys.setenv(PATH = <your new path string>)
Note that system2() is recommended over system() nowadays - but for reasons unimportant for your case. See ?system and ?system2 for a comparison.
Examples
Terminal
$ which node
/usr/bin/node
R
system('/usr/bin/node script.js')
# alternatively:
system2('/usr/bin/node', c('script.js'))
or adapt your PATH permanently:
Terminal
% echo $PATH
/usr/local/bin:/home/caspar/programs:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
R
> Sys.getenv('PATH')
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/RStudio.app/Contents/MacOS/postback"
> Sys.setenv(PATH = "/home/caspar/programs:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/RStudio.app/Contents/MacOS/postback")
I am trying to run an executable called swat_edit.exe in R. It works perfectly when I run it directly in the command prompt, and also when I run it directly in the Terminal tab in R. However, when I try to write a function in R to run the executable, I get an error (I get a number of different errors...).
I have tried to use different methods of running the file:
1: I used system("swat_edit"), which returns the following error:
Unhandled Exception: System.IO.IOException: The handle is invalid.
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.Console.set_CursorVisible(Boolean value)
at SWEdit.Program.Run(String[] args)
at SWEdit.Program.Main(String[] args)
[1] 17234
2: I used shell("swat_edit"), which returns the exact same error as (1).
3: I used shell.exec("swat_edit"). This works, but it opens the executable in a new window, which then runs for a few seconds and closes (as intended). I need the program to run in the R terminal window so it can run many iterations in the background without disrupting other things. This is not a viable option.
4: I tried using terminalSend(ID,"swat_edit") (from the rstudioapi package). This works in that it sends the command to the terminal window in R. When I move there and hit enter it executes perfectly, running in the terminal window like I want it to. However, I need to run many iterations so this is not viable either. I tried using KeyboardSimulator to go to the Terminal tab and hitting enter (which worked), but this also does not let me use the PC for other purposes while running my code.
5: I tried using terminalExecute("swat_edit"), which returns the following error code:
Error calling capture_console_output: 87
[Process completed]
[Exit code: -532462766]
6: I tried making a python file that runs swat_edit.exe, and then running that file in R. The python file works when I run it by itself, from the command prompt, or from the terminal in R. It does not, however, work when I try to run it in the R terminal using terminalExecute (same error as in (5)).
NOTE: I have another executable called swat.exe (entirely different program) that works with all of the above-mentioned methods.
So in summary: swat_edit.exe runs perfectly in command prompt and R terminal, but does not work when I try to run it using R code (either system(), shell(), or terminalExecute().
I can't figure out the difference between terminalExecute() and typing the string into terminal and hitting enter, but apparently there is something happening in between...
It will be tedious to reproduce this since it uses external programs, but if anyone has any idea about the error messages or how I can copy a string and run it in the terminal without any interference, that would be greatly appreciated.
EDIT: I found a method that solves my problem. I created a .bat file that runs swat_edit minimized. I was able to run this .bat file with the shell function (or any of the other commands I mentioned) in R. This doesn't answer why I was having the issues I described, and it doesn't let me run swat_edit in the R terminal, but it's good enough for me.
The .bat file was simply the following:
"START /MIN /WAIT C:\~\SWAT_Edit.exe"
I work with Rscript on a cluster. qmake (a specialized version of GNU-make for the cluster) is used to parallelize jobs on several nodes. But Rscript seems to need to write a Xauthority file and it creates an error when every nodes work in the same time. In this way, my makefile-bases pipeline stops after the first group of parallelized tasks and don't start the next group of tasks. But the results of the first group are ok.
I'm also invoking usr/bin/xvfb-run ( https://en.wikipedia.org/wiki/Xvfb) when runnning RScript.
I've already changed the ssh-config (FORWARD X11 yes) but the problem persists.
I also tried to change the name of Xauthority file for each job but it didn't work (option -f in Rscript).
Here is the error which appear at the beginning of the process
/usr/bin/xauth: error in locking authority file .Xauthority
Here is the error which appears before the process stops :
/usr/bin/xvfb-run: line 171: kill: (44402) - No such process
qmake: *** [Data/Median/median_B00FTXC.tmp] Error 1
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.