I have tested RSWAT with "windows" and "unix", haven't test with Linux. The error in here could be because the way R call the executable file.
Could you run the following command in R (text in red) and give me the screenshot of the R console:
.Platform$OS.type
And you set your TxtInOut as your working directory and and run swat using the following R code
setwd("path_to_your_txtinout")
system("swat2012_681_gfort_linux.exe")