Passing command line arguments to R CMD BATCH

Question

I have been using R CMD BATCH my script R from a terminal to execute an R script   I am now at the point where I would like to pass an argument to the command  but am having some issues getting it working   If I do R CMD BATCH my script R blabla then blabla becomes the output file  rather than being interpreted as an argument available to the R script being executed   I have tried Rscript my script R blabla which seems to pass on blabla correctly as an argument  but then I don t get the my script Rout output file that I get with R CMD BATCH  I want the  Rout file    While I could redirect the output of a call to Rscript to a file name of my choosing  I would not be getting the R input commands included in the file in the way R CMD BATCH does in the  Rout file     So  ideally  I m after a way to pass arguments to an R script being executed via the R CMD BATCH method  though would be happy with an approach using Rscript if there is a way to make it produce a comparable  Rout file

User · Answer

My impression is that R CMD BATCH is a bit of a relict  In any case  the more recent Rscript executable  available on all platforms   together with commandArgs   makes processing command line arguments pretty easy   As an example  here is a little script -- call it  myScript R       myScript R args  lt - commandArgs trailingOnly   TRUE  rnorm n as numeric args 1    mean as numeric args 2      And here is what invoking it from the command line looks like   gt  Rscript myScript R 5 100  1   98 46435 100 04626  99 44937  98 52910 100 78853     Edit   Not that I d recommend it  but     using a combination of source   and sink    you could get Rscript to produce an  Rout file like that produced by R CMD BATCH   One way would be to create a little R script -- call it RscriptEcho R -- which you call directly with Rscript   It might look like this      RscriptEcho R args  lt - commandArgs TRUE  srcFile  lt - args 1  outFile  lt - paste0 make names date       Rout   args  lt - args -1   sink outFile  split   TRUE  source srcFile  echo   TRUE    To execute your actual script  you would then do   Rscript RscriptEcho R myScript R 5 100  1   98 46435 100 04626  99 44937  98 52910 100 78853   which will execute myScript R with the supplied arguments and sink interleaved input  output  and messages to a uniquely named  Rout   Edit2  You can run Rscript verbosely and place the verbose output in a file   Rscript --verbose myScript R 5 100  gt  myScript Rout

User · Answer

In your R script  called test R   args  lt - commandArgs trailingOnly   F  myargument  lt - args length args   myargument  lt - sub  -     myargument  print myargument  q save  no     From the command line run   R CMD BATCH -4 test R   Your output file  test Rout  will show that the argument 4 has been successfully passed to R   cat test Rout   gt  args  lt - commandArgs trailingOnly   F   gt  myargument  lt - args length args    gt  myargument  lt - sub  -     myargument   gt  print myargument   1   4   gt  q save  no    gt  proc time   user  system elapsed  0 222   0 022   0 236

User · Answer

I add an answer because I think a one line solution is always good  Atop of your myRscript R file  add the following line   eval parse text paste commandArgs trailingOnly   TRUE   collapse          Then submit your script with something like   R CMD BATCH  options   --args arguments you want to supply  myRscript R  amp    For example   R CMD BATCH --vanilla  --args N 1 l list a 2  b  test   name  aname   myscript R  amp    Then    gt  ls    1   N      l      name

User · Answer

After trying the options described here  I found this post from Forester in r-bloggers   I think it is a clean option to consider    I put his code here   From command line    R CMD BATCH --no-save --no-restore  --args a 1 b c 2 5 6   test R test out  amp    Test R    First read in the arguments listed at the command line args  commandArgs TRUE      args is now a list of character vectors    First check to see if arguments are passed     Then cycle through each element of the list and evaluate the expressions  if length args   0       print  No arguments supplied          supply default values     a   1     b   c 1 1 1   else      for i in 1 length args          eval parse text args  i              print a 2  print b 3    In test out   gt  print a 2   1  2  gt  print b 3   1   6 15 18   Thanks to Forester

User · Answer

Here s another way to process command line args  using R CMD BATCH   My approach  which builds on an earlier answer here  lets you specify arguments at the command line and  in your R script  give some or all of them default values   Here s an R file  which I name test R   defaults  lt - list a 1  b c 1 1 1      default values of any arguments we might pass     parse each command arg  loading it into global environment for  arg in commandArgs TRUE     eval parse text arg       if any variable named in defaults doesn t exist  then create it    with value from defaults for  nm in names defaults     assign nm  mget nm  ifnotfound list defaults  nm      1     print a  print b    At the command line  if I type  R CMD BATCH --no-save --no-restore  --args a 2 b c 2 5 6   test R   then within R we ll have a   2 and b   c 2 5 6    But I could  say  omit b  and add in another argument c   R CMD BATCH --no-save --no-restore  --args a 2 c  hello   test R   Then in R we ll have a   2  b   c 1 1 1   the default   and c    hello    Finally  for convenience we can wrap the R code in a function  as long as we re careful about the environment      defaults should be either NULL or a named list parseCommandArgs  lt - function defaults NULL  envir globalenv        for  arg in commandArgs TRUE       eval parse text arg   envir envir     for  nm in names defaults       assign nm  mget nm  ifnotfound list defaults  nm     envir envir   1    pos envir        example usage  parseCommandArgs list a 1  b c 1 1 1

User · Answer

You need to put arguments before my script R and use - on the arguments  e g   R CMD BATCH -blabla my script R   commandArgs   will receive -blabla as a character string in this case  See the help for details     R CMD BATCH --help Usage  R CMD BATCH  options  infile  outfile   Run R non-interactively with input from infile and place output  stdout and stderr  to another file   If not given  the name of the output file is the one of the input file  with a possible   R  extension stripped  and   Rout  appended   Options    -h  --help        print short help message and exit   -v  --version     print version info and exit   --no-timing           do not report the timings   --            end processing of options  Further arguments starting with a  -  are considered as options as long as  --  was not encountered  and are passed on to the R process  which by default is started with  --restore --save --no-readline   See also help  BATCH   inside R

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