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I am trying to run a Java application (beagle2vcf) from R.

I tried with system() but no runs are performed only the help of the function is returned in the R console. But when I copy the same command to my cmd console the run is performed.

Then I try with system2() and only output in the console is created, but I need a file on my filesystem.

I am using the stdout parameter, but this does not seem to work.

Perhaps the fact that the Java application uses ">output" to generate files plays a role? Other Java applications that do not have this syntax to output the results run fine with system().

Example of command using system(): 

"java -jar beagle2vcf.jar 1 OneChrom.markers beagleTrain.bgl NA Chrom1Train.vcf"

Example system2 call: 

system2(command="java",args=c("-jar","beagle2vcf.jar", j,"OneChrom.markers","beagleTrain.bgl","NA"),stdout=outnameTrainVCF,invisible=TRUE)

I run R3.5.0 on a windows 10 machine

The output should be a vcf file on my file system.

Rui Barradas
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Koen
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  • Thank you Rui Barradas for formatting my post (new user here, so no idea if this is the appropriate way to thank someone for this)! – Koen May 20 '19 at 11:41

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