R help - Dec 2015 - How to bypass the pause in a program invoked using the "system" command

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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You cannot, in general.  If the program is written to process the stdin input
you might be able to feed it input that it expects, but many DOS/Windows console
programs use BIOS to directly access the keyboard.
-- 
Sent from my phone. Please excuse my brevity.

On December 16, 2015 5:20:44 PM PST, Zhiqiu Hu <zhiqiu.hu at gmail.com>
wrote:
>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.
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
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