I want to run R files in batch mode using Rscript, however it does not seem to be loading the libraries that I need. The specific error I am getting is:

Error in library(timeSeries) : there is no package called 'timeSeries'
Execution halted

However I do have the package timeSeries and can load it from Rstudio, RGui, and R from the command line no problem. The issue seems to only be when running a script using Rscript.

My system/environment variables are configured as:

C:\Program Files\R\R-3.1.0\bin\x64 (Appended to PATH)
R_HOME = C:\Program Files\R\R-3.1.0
R_User = Patrick

I am running the same version of R in RStudio, RGui, and R from command line. I've also checked .Library from these three sources and got the same output as well.

How can I run Rscript from command line with the packages that I am using (and have installed) in R?

EDIT:

I am using Rscript via Rscript script.r at the windows command line in the directory where script.r is located.

The output of Rscript -e print(.Library) is [1] "C:/PROGRA~1/R/R-31~1.0/library"

which is consistent with the other three options that I mentioned: [1] "C:/PROGRA~1/R/R-31~1.0/library"

However, if I put this in my script:

print(.libPaths()) 
library(timeSeries) #This is the package that failed to load

I get an output of:

[1] "C:/Program Files/R/R-3.1.0/library"
Error in library(timeSeries) : there is no package called 'timeSeries'
Execution halted

The corresponding call in RStudio gives an additional path to where the package is actually installed:

> print(.libPaths())
[1] "C:/Users/Patrick/Documents/R/win-library/3.1" "C:/Program Files/R/R-3.1.0/library"    

  

Solution 1:

In short, the value returned by calling Sys.getenv('R_LIBS_USER') in R.exe needs to be the same as the value returned by calling this at the command line:

Rscript.exe -e "Sys.getenv('R_LIBS_USER')"

and the above value needs to be included in this command line call:

Rscript.exe -e ".libPaths()"

Note that the values of R_LIBS_USER may be differ between R.exe and Rscript.exe if the value of R_USER is changed, either in the .Rprofile or the in target field of user's shortcut to R.exe, and in general, I find that the user library (i.e. .libPaths()[2]) is simply not set in Rscript.exe

Since I'm fond of setting R_USER to my USERPROFILE, I include the following block in at the top of .R files that I wish to run on mulitiple computers or in Rscript.exe's .Rprofile (i.e. Rscript -e "path.expand('~/.Rprofile')"):

# =====================================================================
# For compatibility with Rscript.exe: 
# =====================================================================
if(length(.libPaths()) == 1){
    # We're in Rscript.exe
    possible_lib_paths <- file.path(Sys.getenv(c('USERPROFILE','R_USER')),
                                    "R","win-library",
                                    paste(R.version$major,
                                             substr(R.version$minor,1,1),
                                             sep='.'))
    indx <- which(file.exists(possible_lib_paths))
    if(length(indx)){
       .libPaths(possible_lib_paths[indx[1]])
    }
    # CLEAN UP
    rm(indx,possible_lib_paths)
}
# =====================================================================

Solution 2:

As mentioned in the comments, it seems Rscript doesn't recognize the library path defaults automatically. I am writing an R script that needs to be source-able from the command line on different people's computers, so I came up with this more general workaround:

• First store the default library path in a variable (Rscript-sourced functions can find this, they just don't automatiocally)
• Then include that path in the library() call with lib.loc = argument.

• This should work regardless of what the path is on a given computer.

  library.path <- .libPaths()
  library("timeseries", lib.loc = library.path)
  

Thanks again to @flodel above for putting me on the right path

Solution 3:

This answer will not help the original asker (pbreach), but it may help someone else who stumbles across this question and has a similar problem to me.

I have many bash .sh script files which call RScript to execute .R files. My operating system is Windows 10, and I execute those bash files using cygwin.

Everything had been working fine until yesterday, when I finally upgraded my R from Revolution R 8.0.1 beta to Microsoft R Open 3.4.1. After that upgrade, every bash script that called RScript failed due to the exact same reason asked here (e.g. Error in library(zoo) : there is no package called 'zoo').

Investigation revealed that RScript actually worked fine if called from a DOS shell instead of from a cygwin bash shell.

For example, if I execute this in a DOS shell

C:\Progra~1\Microsoft\ROpen~1\R-3.4.1\bin\x64\Rscript.exe -e ".libPaths()"

I see the output

[1] "C:/Users/HaroldFinch/Documents/R/win-library/3.4"
[2] "C:/Program Files/Microsoft/R Open/R-3.4.1/library"

I eventually discovered the reason. As explained in the R FAQ, to define its home directory, R will first use the R_USER environment variable if defined, else it will use HOME environment variable if defined, else it will use the Windows "personal" directory.

My Windows configuration does not define either R_USER or HOME environment variables. So, in the DOS shell case, R uses my Windows "personal" directory (C:/Users/HaroldFinch/Documents). That is good, because that is where all my libraries are installed (C:/Users/HaroldFinch/Documents/R/win-library/3.4).

In contrast, cygwin defines and exports a HOME environment variable that points to my cygwin user directory, which lacks any R stuff. Hence, RScript called from cygwin had a wrong R home directory, and so failed to load libraries.

There are probably many ways to solve this. I decided to have my bash script set a R_USER environment variable which points to my Windows user directory.

For example, if I execute this in a cygwin bash shell:

R_USER="C:/Users/HaroldFinch/Documents"
export R_USER
/cygdrive/c/Progra~1/Microsoft/ROpen~1/R-3.4.1/bin/x64/Rscript.exe -e ".libPaths()"

I see the output

[1] "C:/Users/HaroldFinch/Documents/R/win-library/3.4"
[2] "C:/Program Files/Microsoft/R Open/R-3.4.1/library"

which is exactly the same output now as the DOS shell example above.