[R] How to bypass the pause in a program invoked using the "system" command

[Zhiqiu Hu]

Dear Friends,

I want to run a standalone console program (emBayesB) from R script on
windows console. However, because the program asks user to press the enter
key at each time after the analysis, the R code always stuck after invoking
the emBayesB program with the "system()" function.

For reproduce the issue,  please save the following content as
a "c:\RScript.R" file
##### start ########
AppPath="c:\\bin\\emBayesB_gs.exe"
system(AppPath, wait = TRUE)
##### end ##########

And copy the "emBayesB_gs.exe" file into "c:\\bin". The emBayesB program is
freely accessible at (additional file 3)  the follow website
http://www.biomedcentral.com/1471-2105/11/529/additional

Then, if you try to run the following command on windows console, you will
see the issue.
#####  start of console command  ##########
c:\\R\\bin\\Rscript.exe c:\\RScript.R
#####  end of console command  ##########

FYI, if you submit the "c:\\R\\bin\\Rscript.exe c:\\RScript.R" use the
"system()" function in R (tested with R-studio), you will not required to
press the enter key to finish the run.

Although, the emBayesB program was used in my case, but I suppose it is a
general issue as you call any standalone program that require users
to press key to exit, by run R scripts on windows console .

Any suggestion is appreciated!

Please let me know if you require more information about the issue.

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