After four years of using R, I finally have run into a problem to which I
can't find a solution in the guides or forums and thus I am making my first
post.
Our lab has Fortran code for population modeling. I have been using R as a
wrapper to process the raw data, generate a batch script that compiles the
Fortran code, executes the code in a shell, and then extracts the output of the
program for further analysis and plotting in R.
Because the Fortran modeling program can sometimes take hours or days to
complete, depending on the complexity of the data and model, I want it to run
outside of R to avoid tying it up. In Mac/Unix, I have been able to accomplish
with a function that creates the batch script and then executes it with this
command:
system(paste("open -a Terminal.app
",shQuote(paste(getwd(),"/npscript",sep="")),sep=""))
This opens an independent instance of Terminal and executes the batch script.
The user can provide input to the Fortran executables created/called by the
batch script as required, and see the output in real time as the progress of the
modeling is continually updated.
In Windows, I have been unable to accomplish this. I can generate the batch
script code of course, and it runs perfectly in a command prompt window if I
manually double-click it to execute. However, if I try to execute it from R, I
appear to have no stdin capability (i.e. no user input possible) to the compiled
Fortran executable and no stdout from the executable, i.e. no way to tell if the
Fortran code is hung up, or simply churning away without updating the command
prompt window. It does complete successfully with the expected output files,
but for a long run, it is imperative to view progress normally reported by the
executable.
Here are the first few lines of the batch script that I generate in R,
simplified and with added line numbers for clarity:
1) C:\bin\prep.exe DOS < control #run the prep program with command line arg
to specify OS and input from control (also generated in R with user options to
the function) to automate; no output visible in command prompt window; if
control not specified, then executable waits for user keyboard input, resulting
in a frozen blank window
2) gfortran -o C:\bin\run.exe file1 file2 file 3 prepout... #compile
"engine" files to run model with output of prep program; output
visible in command prompt window
3) C:\bin\run.exe #execute engine to run the model; no output visible
I have tried the following without success:
system("npscript.bat", wait=F, invisible=F) and all permutations
system2("npscript.bat", wait=F, invisible=F) and all permutations
shell("npscript.bat")
shell("start npscript.bat")
Is there any way to replicate the Unix behavior in Windows and launch a shell
that runs the batch script with the same I/O capability as if I had manually
launched it? Yes, I could have users manually launch the batch script, but it
would be tidier if R could successfully complete the process.
Thanks very much.
