I have two R scripts. one is: source("D:/source_code_CCA.r") and another one is: source("D:/source_code_DL.r"). These two R scripts are completely independent. I want to run these two r scripts at a time on same R console on windows. How can I do this? Please help!
You could create a new script containing the following lines, or execute them via interactive console -- after making sure that the directory containing Rscript.exe is in your PATH:
shell(cmd = 'Rscript.exe D:/source_code_cca.r', wait=FALSE)
shell(cmd = 'Rscript.exe D:/source_code_DL.r', wait=FALSE)
(If it's not already there, the value to add to path could be C:\Program Files\R\R-3.1.2\bin or C:\Program Files\R\R-3.1.2\bin\x64)
Note that if you use cats or messages, those would be captured if you direct them to a text file, such as in:
shell(cmd = 'Rscript.exe D:/source_code_cca.r > out1.log', wait=FALSE)
shell(cmd = 'Rscript.exe D:/source_code_DL.r > out2.log', wait=FALSE)
Or if you specify intern=TRUE and assign the function's result to some variable:
res1 <- shell(cmd = 'Rscript.exe D:/source_code_cca.r', wait=FALSE, intern=TRUE)
res2 <- shell(cmd = 'Rscript.exe D:/source_code_DL.r', wait=FALSE, intern=TRUE)
I believe you're using Windows, the path tells me :-)
Open two different cmd.exe windows.
Use the R command to call one of the script in the first window, and one for the second. This can be done with some minor magic like: R.exe --no-environ --no-save > "out.txt"
Hope that helps. Alternatively, you can spawn different processed if you want to call them within the same shell.
Related
I am trying to execute a R script from node.js using r-script because it looks pretty simple.
With the documentation example:
example.js
var out = R("ex-sync.R")
.data("hello world", 20)
.callSync();
console.log(out);
ex-sync.R
needs(magrittr)
set.seed(512)
do.call(rep, input) %>%
strsplit(NULL) %>%
sapply(sample) %>%
apply(2, paste, collapse = "")
My out variable which supposed to be the last line of R script, is always null and I have no idea why this can happen.
For Windows users:
You need to add the environment variable to Windows's %PATH% variable. R-script package needs to call "R" command from the CMD. If R.exe is not set as an environment variable, then it will never be able to call the "R" command from anywhere.
Look up how to add environment variables to Windows, and remember: if the path to the folder containing the executables has a white space, it must be added to double quotes. "C:\Program Files\R\R-version\bin\x64"
**** replace version**
If you have already done this but the problem persists, I can only think of two reasons:
There's something wrong with your R method and it's giving an internal exception inside the R session.
The system can't find the file. Maybe check the file path.
I've a batch file that calls R script. It works fine. I need to know how Can I Call a function in R Script from that Batch file in windows? How to call this Function with parameters:
PNLCalcMultipleDatesClient("2010-10-03", "2010-10-05", "XYZ")
This command line works but it doesn't have Function call that is in R Script. Can you please help me to modify this command line in Windows and call above function ?
"\\C1PRDTLS01.axinc.com\Dev\RiskClient\inputCData\PNLCalculation\R\R-3.1.1\bin\R.exe" CMD BATCH --no-save --no-restore "\\C1PRDTLS01.axinc.com\Dev\RiskClient\inputCData\PNLCalculation\RScript\RadarPNLTimeseries.R"
Here is the R Script:
PNLCalcMultipleDatesClient("2010-10-03", "2010-10-05", "Dunavant")
PNLCalcMultipleDatesClient <- function(begindate, enddate, Client)
{
# Do some operation here....
.....
......
}
Here is an example. Here is the Rscript that i have, i tend to save them as txt itself.
## Rscript: Passing arguments to the Rscripts likes args[i]
#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
print(1:args[1])
df=data.frame(1:args[1])
write.csv(df, args[2])
Then your batch file would look like this. Then you feed those arguments either directly to a cmd or create a batch file out of it.
echo off
Rscript rparam.txt 1000 out.csv
For your case, your Rscript(R_with_par.R) would be:
#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
x1=args[1]
x2=args[2]
x3=args[3]
PNLCalcMultipleDatesClient <- function(begindate, enddate, Client)
{
# Do some operation here....
.....
......
}
PNLCalcMultipleDatesClient(as.Date(x1), as.Date(x2), as.character(x3))
And your CMD command would be:
Rscript R_with_par.R 2010-10-03 2010-10-05 Dunavant
You have to make sure that parameters that you pass are in format required by R. Give the path of the R script if you are not in the same directory. Also Rscript is far better choice than R CMD.
Create R Function:
squared <- function(number) {
sqred <- number^2
cat(sqred)
}
squared(as.integer(commandArgs(trailingOnly = TRUE)))
Run R script from command prompt: (Your path could be different)
C:R/bin/RScript.exe" "C:/Rscript/command_line.R" 100
Note: First argument is path of Rscript.exe, Second Argument is path of your R script and third argument is function argument.
I have an inconsistency issue which I cannot explain when running an R script. I am not able to produce a reproducible example because there is a whole set of files/functions called by the entry script.
Using Rscript or RStudio with R v3.1.2 I obtain the results I'm expecting, however when calling R CMD BATCH from bash my script does not produce identical output. From bash, R seems to read the command line arguments correctly and reports them from the script, BUT in my code only the Rscript and RStudio source methods seem to use the parameter correctly in my code.
The 2 command line calls are as follows:
Rscript ./script/forecast_category_script.R "category='razors'" "cores=4L"
R CMD BATCH --no-save "--args category='razors' cores=4L" ./script/forecast_category_script.R ~/data/output/out.out
Is there any obvious reason why these inconsistencies might be occurring? I'd prefer to use R CMD BATCH as it redirects output to a file and when I migrate my code to the university cluster as a batch job through the scheduler I'd like to be able to follow what it has done.
UPDATE: changing this line resolves it but why?
Previously I had the following line in there, basically so when I was testing I didn't keep reloading the huge dataset if it was already loaded in my RStudio environment:
if(!exists("spi")) spi = f_load.spi(category = category)
Replaced it with this:
spi = f_load.spi(category = category)
The underlying function f_load_spi remained the same however:
f_load.spi = function(spi = NULL, category = "razors" , n=NULL) {
# check if the data is pre-loaded
if (is.null(spi)) {
fil = paste0(pth.data.storage, "categories/", category, "/", category, ".sp_ss.interp.rds")
print(fil)
spi = readRDS(fil)
}
# subset to a specific set of items
if (!is.null(n)) {
fc.items = unique(spi$fc.item)
rnd = sample(1:length(fc.items), n)
spi = spi[fc.item %in% fc.items[rnd]]
}
spi
}
For some reason the category variable was not being passed through properly into the function and it was loading a different category (beer rather than razors) which was an enormous file and not suitable for testing.
This still doesn't explain why Rscript and R CMD BATCH behaved differently.
It is possible that one of them is loading up a previously saved workspace and using global variables. Have you checked whether it matters which directory you are in or if there are any .Rhistory files present? One way to ensure that you don't have any hidden variables is to clear the worspace at the beginning of each script. For example, rm(list=ls()) as the first line of your Rscript.
Also, you can pipe output to a file with an Rscript using sink().
I am trying to run an R script from the Windows command prompt (the reason is that later on I would like to run the script by using VBA).
After having set up the R environment variable (see the end of the post), the following lines of code saved in R_code.R work perfectly:
library('xlsx')
x <- cbind(rnorm(10),rnorm(10))
write.xlsx(x, 'C:/Temp/output.xlsx')
(in order to run the script and get the resulting xlsx output, I simply type the following command in the Windows command prompt: Rscript C:\Temp\R_code.R).
Now, given that this "toy example" is working as expected, I tried to move to my main goal, which is indeed very similar (to run a simple R script from the command line), but for some reason I cannot succeed.
Again I have to use a specific R package (-copula-, used to sample some correlated random variables) and export the R output into a csv file.
The following script (R_code2.R) works perfectly in R:
library('copula')
par_1 <- list(mean=0, sd=1)
par_2 <- list(mean=0, sd=1)
myCop.norm <- ellipCopula(family='normal', dim=2, dispstr='un', param=c(0.2))
myMvd <- mvdc(myCop.norm,margins=c('norm','norm'),paramMargins=list(par_1,par_2))
x <- rMvdc(10, myMvd)
write.table(x, 'C:/Temp/R_output.csv', row.names=FALSE, col.names=FALSE, sep=',')
Unfortunately, when I try to run the same script from the command prompt as before (Rscript C:\Temp\R_code2.R) I get the following error:
Error in FUN(c("norm", "norm"))[[1L]], ...) :
cannot find the function "existsFunction"
Calls: mvdc -> mvdcCheckM -> mvd.has.marF -> vapply -> FUN
Do you have any idea idea on how to proceed to fix the problem?
Any help is highly appreciated, S.
Setting up the R environment variable (Windows)
For those of you that want to replicate the code, in order to set up the environment variable you have to:
Right click on Computer -> Properties -> Advanced System Settings -> Environment variables
Double click on 'PATH' and add ; followed by the path to your Rscript.exe folder. In my case it is ;C:\Program Files\R\R-3.1.1\bin\x64.
This is a tricky one that has bitten me before. According to the documentation (?Rscript),
Rscript omits the methods package as it takes about 60% of the startup time.
So your better solution IMHO is to add library(methods) near the top of your script.
For those interested, I solved the problem by simply typing the following in the command prompt:
R CMD BATCH C:\Temp\R_code2.R
It is still not clear to me why the previous command does not work. Anyway, once again searching into the R documentation (see here) proves to be an excellent choice!
I call a script from a shell command line with
r CMD BATCH myscript.R
What do I have to do in myscript.R to get a character vector with the name of the script (i.e. "myscript.R")?
Note:
I found numerous questions on similar topics, but couldn't find anything that work for me. Particularly from question Determine path of the executing script I got the modified script snippet:
args <- commandArgs(trailingOnly = F)
scriptPath <- sub("^--file=", "", args[grep("^--file=", args)])
but scriptPath is always empty (probably due to the way I call the script via the BATCH command).
A simple example with commandArgs() works fine for me:
myscript.R:
commandArgs()[3]
in the terminal:
R CMD BATCH myscript.R
and then cat myscript.Rout:
commandArgs()[3]
[1] "myscript.R"
I believe if you use Rscript instead of R CMD BATCH it will work for you. I read the same post when I was trying to figure out how set working directory to directory of myscript. Anyway to run Rscript
"....\R-3.0.1\bin\x64\Rscript.exe" Myscript.r > Myscript.r.rout
And here is my code to set working directory to directory of script. I kept trying different alternatives to this then I realized you need to be using Rscript for the bulk of them to work.
args <- commandArgs(trailingOnly = F)
scriptPath <- normalizePath(dirname(sub("^--file=", "", args[grep("^--file=", args)])))
setwd(scriptPath)