Run R silently from command line, export results to JSON -


how might call r script shell (e.g. node.js exec) , export results json (e.g. node.js)?

the r code below works. reads data, fits model, converts parameter estimates json, , prints them stdout:

#!/usr/bin/rscript --quiet --slave install.packages("cut", repos="http://cran.rstudio.com/"); install.packages("hmisc", repos="http://cran.rstudio.com/"); install.packages("rjson", repos="http://cran.rstudio.com/"); library(rjson) library(reshape2);  data = read.csv("/data/records.csv", header = true, sep=","); mylogit <- glm( y ~ x1 + x2 + x3, data=data, family="binomial"); params <- melt(mylogit$coefficients); json <- tojson(params); json

here's how i'd call node...

var exec = require('child_process').exec; exec('./model.r', function(err, stdout, stderr) {    var params = json.parse(stdout);  // fail! junk in stdout        });

except r process won't stop printing stdout. i've tried --quiet --slave --silent little not enough. here's what's sent stdout:

the downloaded binary packages in     /var/folders/tq/frvmq0kx4m1gydw26pcxgm7w0000gn/t//rtmpyk7gmn/downloaded_packages  downloaded binary packages in     /var/folders/tq/frvmq0kx4m1gydw26pcxgm7w0000gn/t//rtmpyk7gmn/downloaded_packages [1] "{\"value\":[4.04458733165933,0.253895751245782,-0.1142272181932,0.153106007464742,-0.00289013062471735,-0.00282580664375527,0.0970325223603164,-0.0906967639834928,0.117150317941983,0.046131890754108,6.48538603593323e-06,6.70646151749708e-06,-0.221173770066275,-0.232262366060079,0.163331098409235]}"

what's best way use r scripts on command line?

running r --silent --slave cmd batch model.r per post below still results in lot of extraneous text printed model.rout:

run r script command line

those options stop r's own system messages printing, won't stop r function doing printing. otherwise you'll stop last line printing , won't json stdout!

those messages coming install.packages, try:

 install.packages(-whatever-, quiet=true)

which claims reduce amount of output. if reduces zero, job done.

if not, can redirect stdout sink, or run things inside capture.output.


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