R -- For loop using sprintf function in command system evaluation - r

Question

I have a number of files that I would like to run using a batch file that will be executed from R using a for loop. As an example, let's assume that I have 2 runs that I would like to execute:
runs <- c(102, 103)
The syntax for the system command requires that the batch file be specified first, followed by the input data file for the run (102.txt and 103.txt) and the name of the output results file after the batch file has been executed (102.res and 103.res). I am attempting to run this using a for loop:
for (r in runs) {
cmd <- sprintf('C:/example1/test.bat %d.txt %d.res', runs, runs)[1]
print(eval(cmd))
command: system(cmd)
}
[1] "C:/example1/test.bat 102.txt 102.res"
Unfortunately, this only executes the first run (102) and does not advance to the next run (103). The R console displays the following warning:
Error in command:system(cmd) : NA/NaN argument
Thinking that this error is what is preventing R from advancing to the next run, I have attempted to use options(warn = -1) in the for loop:
for (r in runs) {
options(warn = -1)
cmd <- sprintf('C:/example1/test.bat %d.ctl %d.res', runs, runs)[1]
print(eval(cmd))
command: system(cmd)
options(warn = 0)
}
Unfortunately, this continues to throw the same error. For what it's worth, the output from my batch file (102.res) is exactly how I want it to be, I simply want to be able to bypass this error and continue on with the rest of my runs. Any thoughts on how best to do that?
Thanks in advance.

Answer 1

Here's what you had
runs <- c(102, 103)
for (r in runs) {
cmd <- sprintf('C:/example1/test.bat %d.txt %d.res', runs, runs)[1]
print(eval(cmd))
# command: system(cmd)
}
which outputs
[1] "C:/example1/test.bat 102.txt 102.res"
[1] "C:/example1/test.bat 102.txt 102.res"
try using the loop variable, r, instead of the array, runs, in the cmd <-... line
for (r in runs) {
cmd <- sprintf('C:/example1/test.bat %d.txt %d.res', r, r)[1] # <- change runs to r
print(eval(cmd))
# command: system(cmd)
}
output is
[1] "C:/example1/test.bat 102.txt 102.res"
[1] "C:/example1/test.bat 103.txt 103.res"