similar to: R's parsing of command line arguments using commandArgs()

Displaying 20 results from an estimated 10000 matches similar to: "R's parsing of command line arguments using commandArgs()"

2011 Mar 14
1
Rscript, hashbang, and arguments
Hi, I have a bunch of R scripts which have the hash bang !/usr/bin/env Rscript and I typically run these scripts by passing in some parameters like this: ./nameOfRScript arg1 arg2 ... I know Rscript has the option to run in --vanilla. Where exactly do I insert the --vanilla option? When I do something like this: ./nameOfRScript --vanilla arg1 arg2 ... And I try to access the commandArgs,
2012 Sep 06
1
[Rscript] difficulty passing named arguments from commandline
Wanting a commandline solution (for a problem detailed @ http://mailman.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2012/msg00279.html ) I turned to Rscript, and whacked out the q'n'd https://github.com/TomRoche/GEIA_to_netCDF/blob/master/netCDF.stats.to.stdout.r However it wasn't as quick as hoped, because I spent quite a bit of time figuring out how to pass the arguments.
2014 Sep 18
1
last user argument missing from Rscript --verbose
The loop that echoes the arguments almost always stops too soon. It apparently does that to avoid echoing the "--args" (that had been inserted) when there are no user arguments. However, when there are user arguments, the next element of the 'av' array is the last argument and usually not "--args", although it can be. ?Rscript is a little sketchy: ?--verbose?
2008 Jan 05
1
Rscript argument processing minor bug with -g
I think there's a minor bug in the argument-processing carried out by Rscript. The effect is that if one passes "-g" as a flag to the script, it is erroneously exposed to the main executable's argument processing and therefore generates a message about not being able to comply with the request for a particular GUI. Uppercase G is fine as are the other 25 letters in upper or
2007 Apr 01
2
commandArgs usage and --args invokation
Dear R experts: I am a bit stymied by how the argument picking-off works in R batch file usage. $ cat commandArgs.R cat(" Command Line Arguments were ", commandArgs(), "\n"); $ /usr/bin/R CMD BATCH commandArgs.R --args 1 2 3 $ /usr/bin/R --args 1 CMD BATCH commandArgs.R ... I am now getting into interactive mode ?! I guess it really is skipping the rest of the command line
2018 Sep 16
4
Rscript -e does not accept newlines under Linux?
Hello, I have found what I believe to be a bug in the Linux version of the Rscript binary. Under Windows (official 64-bit 3.5.1 R distribution running on an up-to-date Win10), I can do the following (e.g. under powershell): PS H:\Users\Cesko> Rscript -e 'ls() >> ls()' character(0) character(0) which works as I expect: I am running Rscript with two arguments, namely (1)
2009 Aug 05
1
exec subdirectory of a package
Hello, WRE contains the following information about the "exec" subdirectory of a package : "Subdirectory exec could contain additional executables the package needs, typically scripts for interpreters such as the shell, Perl, or Tcl. This mechanism is currently used only by a very few packages, and still experimental." I think it would be useful to expand "very
2017 Oct 20
1
Rscript Bug Report (improper parsing of [args])
Hi, A user of my `optparse` package discovered a bug in Rscript's parsing of [args]. (https://github.com/trevorld/optparse/issues/24) I've reproduced the bug on my machine including compiling and checking the development version of R. I couldn't find a mention of it in the Bug Tracker or New Features. Can be minimally reproduced on the UNIX command line with following commands:
2017 Dec 05
2
command line arguments are parsed differently on windows, from 3.4.3
Sorry for not reading carefully and thanks for confirming problem with Rscript too. On Dec 5, 2017 08:47, "G?bor Cs?rdi" <csardi.gabor at gmail.com> wrote: > On Tue, Dec 5, 2017 at 4:40 PM, Henrik Bengtsson > <henrik.bengtsson at gmail.com> wrote: > > One comment: > > For your R devel example you didn't use spaces in the expression, i.e. > maybe
2012 May 03
1
is there a way of identifying batch mode running?
Hello list Is there a way of identifying from within R whether a script has been source(d) from Rgui.exe or via Rscript.exe in batch mode? For the code I have I use the commandArgs() function to pick up command line args when running in batch mode via Rscript.exe However I like to get the code working manually first using source("MyRCode.r") I'd like to be able to put something at
2013 Mar 24
0
Rscript does not load/capture all shell arguments
Hi, I am working on a GRASS script (bash script), which should run a R script. I am working on Ubuntu 12.10, with R 2.15.3 and GRASS GIS 7.0 (I am not sure the latter isn't really relevant as the grass script is just a bash script). The R script is evoked with a call to Rscript ($RGRASSSCRIPT is a shell variable with the file name of the R script, the rest are variables I want to read into R)
2017 Dec 05
2
command line arguments are parsed differently on windows, from 3.4.3
One comment: For your R devel example you didn't use spaces in the expression, i.e. maybe that's broken too with spaces? Three questions: Does it work if you avoid spaces? Does it work if you use single quotes? Does this also occur for Rscript? Thxs Henrik On Dec 5, 2017 03:44, "G?bor Cs?rdi" <csardi.gabor at gmail.com> wrote: I wonder if this is intended. Thanks,
2012 Oct 29
6
export variable from bash to R
Dear R experts This probably seems very easy to you guys, but I'm a beginner and would be really glad if someone helped me with this: I am trying to automate the execution of an R script (let's call it "myscript.R") by passing a variable from a bash script to myscript.R. I know I can use the command Rscript, but I don't know how to declare in bash which variable will be
2012 Mar 01
2
Rscript example
Hi there, I am trying to find an example how to use Rscript Let's suppose I want to pass 3 arguments (I don't want [options] and -e [expressions] as described in help) *on the command line myRscript.R -arg1=value1 -arg2=value2 -arg3=value3 *In the script #! /path/to/Rscript args = commandArgs(TRUE); >From what I see args is just a string, do I do things correctly ? -- View this
2009 Aug 20
1
Command line option to an R script running through Rscript
Hi, I know that I can use the following script to get the command line options for an R script. But the output shows two many irrelevant arguments. For example, I only want to pass "a", "b" and "c" to the script. The first 5 elements in the variable 'args' are not what I want. I am wondering what is the correct way to pass command line options to an R script.
2009 Nov 10
1
Is it possible to detect whether running as Rscript?
I would like to write a block of code that runs when a script is being run from Rscript, but not to run if the same file is being source()d, or submitted via ESS, etc. As a gloss I would like to write a file that looks somewhat like: #!/usr/bin/env Rscript my.func <- function(...) { #do something... } if ( #is.running.Rscript# ) { do.call(my.func, commandArgs(trailingOnly=TRUE)) }
2016 Oct 29
3
pasar argumentos de consola a un script de R que contiene source
Hola. Tengo un script con la siguiente estructura. #!/usr/bin/env Rscript args = commandArgs(trailingOnly=TRUE) source("carga-datos.R") source("modelo.R") y quiero llamar a mi script desde consola con Rscript --vanilla miscript.R datos1.csv De forma que se guarde como argumento el nombre del fichero que quiero cargar y se pase a al script carga-datos.R. El problema es
2009 Sep 07
2
Writing R Scripts and passing command line arguments
Hi Guys I am Abhishek, primarily a bioinformatician. I have recently started using a lot of R thanks to some excellent packages available. Lately I have felt the need to batch process few of the R scripts I have been working with and strangely enough I am not able to find a good resource on how to best do this. I did find few old threads on the archives but none convinced me much. So here I am
2009 Aug 28
1
How to convert a string passed as an argument to a vector?
Hi, $ cat commandArgs.R args=commandArgs(trailingOnly=TRUE) args[1]+10 I have the above code. But the following command line gives me an error. I am wondering what is the correct way to convert a string to a vector? $ Rscript commandArgs.R 1:3 > args=commandArgs(trailingOnly=TRUE) > args[1]+10 Error in args[1] + 10 : non-numeric argument to binary operator Execution halted Regards, Peng
2012 Mar 28
2
getopt does not work as expected!
I have the following script (also attached): #!/usr/bin/Rscript spec=matrix(c( 'verbose', 'v', 1, "integer", 'help' , 'h', 0, "logical" ),ncol=4, byrow=TRUE) spec.dim=dim(spec) spec.opt.long=spec[,1] spec.opt.short=spec[,2] spec.opt.l <- spec.dim[1] infile <- "test.dat" args=commandArgs(TRUE); l=length(args) self =