I have a script called foo.R that includes another script other.R, which is in the same directory:
#!/usr/bin/env Rscript
message("Hello")
source("other.R")
But I want R to find that other.R no matter what the current working directory.
In other words, foo.R needs to know its own path. How can I do that?
I've made a package for this, available on CRAN and GitHub, called "this.path". The current version is 0.11.0 published on 2022-09-03, you can find it here:
https://CRAN.R-project.org/package=this.path
https://github.com/ArcadeAntics/this.path
Install it from CRAN with:
utils::install.packages("this.path")
or from GitHub with:
utils::install.packages("this.path", repos = "https://raw.githubusercontent.com/ArcadeAntics/PACKAGES")
and then use it by:
this.path::this.path()
or
library(this.path)
this.path()
The answer below is my original answer, kept just for reference, though it is quite a bit less functional than the most recent versions available above. Improvements include:
this.path() now works within VSCode, see ?this.path.in.VSCode for more informationsource with argument chdir = TRUEsource (that is, "file://absolute or relative path" and "file:///absolute path")sourcethis.path is compatible with URLs in source, that is:source("https://host/path/to/file")
if this.path was used within the file, it would return "https://host/path/to/file". This also works for a URL beginning with "http://", "ftp://", and "ftps://". As an example, try:
source("https://raw.githubusercontent.com/ArcadeAntics/this.path/main/tests/this.path_w_URLs.R")
testthat::source_filehere, similar to here::here, for specifying an absolute file path, relative to the executing script's directorylist.dirs(system.file(package = "translations"), full.names = FALSE, recursive = FALSE)this.path is called within a script, making it faster to use subsequent times within the same script and being independent of working directory. This means that setwd will no longer break this.path when using relative paths within source or when running R from a shell (as long as setwd is used AFTER the first call to this.path within that script)Original Answer:
My answer is an improvement upon Jerry T's answer. The issue I found is that they are guessing whether a source call was made by checking if variable ofile is found in the first frame on the stack. This will not work with nested source calls, nor source calls made from a non-global environment. Additionally, the order is wrong. We must look for source call BEFORE checking the shell arguments. Here is my solution:
this.path <- function (verbose = getOption("verbose"))
{
where <- function(x) {
if (verbose)
cat("Source: ", x, "\n", sep = "")
}
# loop through functions that lead here from most recent to earliest looking
# for an appropriate source call (a call to function source or sys.source)
# an appropriate source call is a source call in which
# argument 'file' has been evaluated (forced)
# this means, for example, the following is an inappropriate source call:
# source(this.path())
# the argument 'file' is stored as a promise
# containing the expression "this.path()"
# when the value of 'file' is requested, it assigns the value
# returned by evaluating "this.path()" to variable 'file'
# there are two functions on the calling stack at
# this point being 'source' and 'this.path'
# clearly, you don't want to request the 'file' argument from that source
# call because the value of 'file' is under evaluation right now!
# the trick is to ask if variable ('ofile' for source, 'exprs' for sys.source)
# exists in that function's evaluation environment. this is because that
# variable is created AFTER argument 'file' has been forced
# if that variable does exist, then argument 'file' has been forced and the
# source call is deemed appropriate. For source, the filename we want
# is the variable 'ofile' from that function's evaluation environment. For
# sys.source, the filename we want is the variable 'file' from that
# function's evaluation environment.
# if that variable does NOT exist, then argument 'file' hasn't been forced and
# the source call is deemed inappropriate. The 'for' loop moves to the next
# function up the calling stack (if available)
#
# unfortunately, there is no way to check the argument 'fileName' has been forced
# for 'debugSource' since all the work is done internally in C. Instead,
# we have to use a 'tryCatch' statement. When we ask for an object by name
# using 'get', R is capable of realizing if a variable is asking for its
# own definition (a recursive definition). The exact error is "promise already
# under evaluation" which indicates that the promise evaluation is requesting
# its own value. So we use the 'tryCatch' to get the argument 'fileName'
# from the evaluation environment of 'debugSource', and if it does not raise
# an error, then we are safe to return that value. If not, the condition
# returns false and the 'for' loop moves to the next function up the calling
# stack (if available)
dbs <- if (.Platform$GUI == "RStudio")
get("debugSource", "tools:rstudio", inherits = FALSE)
for (n in seq.int(sys.nframe(), 1L)[-1L]) {
if (identical(sys.function(n), source) &&
exists("ofile", envir = sys.frame(n), inherits = FALSE)) {
path <- get("ofile", envir = sys.frame(n), inherits = FALSE)
if (!is.character(path))
path <- summary.connection(path)$description
where("call to function source")
return(normalizePath(path, mustWork = TRUE))
}
else if (identical(sys.function(n), sys.source) &&
exists("exprs", envir = sys.frame(n), inherits = FALSE)) {
path <- get("file", envir = sys.frame(n), inherits = FALSE)
where("call to function sys.source")
return(normalizePath(path, mustWork = TRUE))
}
else if (identical(sys.function(n), dbs) &&
tryCatch({
path <- get("fileName", envir = sys.frame(n), inherits = FALSE)
TRUE
}, error = function(c) FALSE)) {
where("call to function debugSource in RStudio")
return(normalizePath(path, mustWork = TRUE))
}
}
# if the for loop is passed, no appropriate
# source call was found up the calling stack
# next, check if the user is running R from a shell
# on a Windows OS, the GUI is "RTerm"
# on a Unix OS, the GUI is "X11"
# if (running R from a shell)
if (.Platform$OS.type == "windows" && .Platform$GUI == "RTerm" || # on Windows
.Platform$OS.type == "unix" && .Platform$GUI == "X11") { # under Unix-alikes
# get all shell arguments that start with "--file="
# check the number of shell arguments starting with "--file="
# in case more or less than one were supplied
path <- grep("^--file=", commandArgs(), value = TRUE)
if (length(path) == 1L) {
path <- sub("^--file=", "", path)
where("shell argument 'FILE'")
return(normalizePath(path, mustWork = TRUE))
}
else if (length(path)) {
stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* R is being run from a shell where formal argument 'FILE' matched by multiple actual arguments")
}
else stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* R is being run from a shell where argument 'FILE' is missing")
}
# if (running R from RStudio)
else if (.Platform$GUI == "RStudio") {
# function ".rs.api.getActiveDocumentContext" from the environment "tools:rstudio"
# returns a list of information about the document where your cursor is located
#
# function ".rs.api.getSourceEditorContext" from the environment "tools:rstudio"
# returns a list of information about the document open in the current tab
#
# element 'id' is a character string, an identification for the document
# element 'path' is a character string, the path of the document
adc <- get(".rs.api.getActiveDocumentContext",
"tools:rstudio", inherits = FALSE)()
if (adc$id != "#console") {
path <- adc$path
if (nzchar(path)) {
where("active document in RStudio")
return(normalizePath(path, mustWork = TRUE))
}
else stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* active document in RStudio does not exist")
}
sec <- get(".rs.api.getSourceEditorContext",
"tools:rstudio", inherits = FALSE)()
if (!is.null(sec)) {
path <- sec$path
if (nzchar(path)) {
where("source document in RStudio")
return(normalizePath(path, mustWork = TRUE))
}
else stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* source document in RStudio does not exist")
}
else stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* R is being run from RStudio with no documents open")
}
# if (running R from RGui on Windows)
else if (.Platform$OS.type == "windows" && .Platform$GUI == "Rgui") {
# on a Windows OS only, the function "getWindowsHandles" from the base
# package "utils" returns a list of external pointers containing the windows
# handles. The thing of interest are the names of this list, these should
# be the names of the windows belonging to the current R process. Since
# RGui can have files besides R scripts open (such as images), a regular
# expression is used to subset only windows handles with names that exactly
# match the string "R Console" or end with " - R Editor". I highly suggest
# that you NEVER end a document's filename with " - R Editor". From there,
# similar checks are done as in the above section for 'RStudio'
wh <- names(utils::getWindowsHandles(pattern = "^R Console$| - R Editor$",
minimized = TRUE))
if (!length(wh))
stop("no windows in RGui; should never happen, please report!")
path <- wh[1L]
if (path != "R Console") {
path <- sub(" - R Editor$", "", path)
if (path != "Untitled") {
where("active document in RGui")
return(normalizePath(path, mustWork = TRUE))
}
else stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* active document in RGui does not exist")
}
path <- wh[2L]
if (!is.na(path)) {
path <- sub(" - R Editor$", "", path)
if (path != "Untitled") {
where("source document in RGui")
return(normalizePath(path, mustWork = TRUE))
}
else stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* source document in RGui does not exist")
}
else stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* R is being run from RGui with no documents open")
}
# if (running R from RGui on macOS)
else if (.Platform$OS.type == "unix" && .Platform$GUI == "AQUA") {
stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* R is being run from AQUA which requires a source call on the calling stack")
}
# otherwise
else stop("'this.path' used in an inappropriate fashion\n",
"* no appropriate source call was found up the calling stack\n",
"* R is being run in an unrecognized manner")
}
I have wrapped up and extended the answers to this question into a new function thisfile() in rprojroot. Also works for knitting with knitr.
I tried almost everything from this question, Getting path of an R script, Get the path of current script, Find location of current .R file and R command for setting working directory to source file location in Rstudio, but at the end found myself manually browsing the CRAN table and found
scriptName library
which provides current_filename() function, which returns proper full path of the script when sourcing in RStudio and also when invoking via R or RScript executable.
I also had this problem, and none of the above solutions worked for me. Maybe with the source or things like that, but it was not clear enough.
I found this, for me elegant, solution:
paste0(gsub("\\", "/", fileSnapshot()$path, fixed=TRUE),"/")
The important thing in that is the fileSnapshot() that gives you a lot of information about a file. It returns a list of 8 elements. When you pick path as the list element, the path is returned with \\ as separator, so the rest of the code is just to change that.
I hope this helps.
By looking at the call stack we can get the filepath of each script being executed, the two most useful will probably either be the currently executing script, or the first script to be sourced (entry).
script.dir.executing = (function() return( if(length(sys.parents())==1) getwd() else dirname( Filter(is.character,lapply(rev(sys.frames()),function(x) x$ofile))[[1]] ) ))()
script.dir.entry = (function() return( if(length(sys.parents())==1) getwd() else dirname(sys.frame(1)$ofile) ))()
I work in an HPC cluster environment. I develop my code in a different location from where I do my production runs. During development, I'm usually calling R interactively from the command line (not using RStudio). There is lots of source("foo.R") going on.
During production runs, I usually write a bash script that tries different parameters and runs each set of parameters in a separate directory. The bash script utilizes the workload manager (i.e. SLURM). In this environment, it is trivial to set an environmental variable. With this in mind, the below solution works best for me.
other.R
my_message <- function(){
return("R is awkward")
}
foo.R
srcpath = Sys.getenv("R_SRC")
# Check if runnning w/o setting R_SRC - presumably done in directory of development, i.e. /path/to/R/code
if(srcpath == ""){
srcpath="./"
}
source(sprintf("%s/other.R", srcpath))
string = my_message()
print(string)
If running this from the R interactive shell and within /path/to/R/code, simply do
> source("foo.R")
If running not from the interactive shell and not running from /path/to/R/code, set the environmental variable R_SRC first, then call Rscript
$ export R_SRC=/path/to/R/code/
$ Rscript /path/to/R/code/foo.R
The solution arrived in 2016. Many thanks to the author, Sahil Seth!
The package funr on CRAN and github provides the function sys.script() which gets the full path to the current script. It even references a similar SO post.
Thus, the solution is:
myscript.R:
#!/usr/bin/env Rscript
f <- funr::sys.script()
show(f)
and then executing the command:
user@somewhere:/home$ Rscript myscript.R
at the command line will output, e.g.:
"/home/path/to/myscript.R"
to the console.
Just to build on the above answers, as a safety check, you could add a wrapper that asks the user to find the file if (for whatever reason) sys.frame(1) fails (as it might if interactive() == TRUE), or the sourced script is not where the main script expects it to be.
fun_path = tryCatch(expr =
{file.path(dirname(sys.frame(1)$ofile), "foo.R")},
error = function(e){'foo.R'}
)
if(!file.exists(fun_path))
{
msg = 'Please select "foo.R"'
# ask user to find data
if(Sys.info()[['sysname']] == 'Windows'){#choose.files is only available on Windows
message('\n\n',msg,'\n\n')
Sys.sleep(0.5)#goes too fast for the user to see the message on some computers
fun_path = choose.files(
default = file.path(gsub('\\\\', '/', Sys.getenv('USERPROFILE')),#user
'Documents'),
caption = msg
)
}else{
message('\n\n',msg,'\n\n')
Sys.sleep(0.5)#goes too fast for the user to see the message on some computers
fun_path = file.choose(new=F)
}
}
#source the function
source(file = fun_path,
encoding = 'UTF-8')