I'm running a new script on R and i'm trying to call a file .exe using the function system() from r.
I run :
system("C:/Program Files (x86)/OxMetrics6/ox/bin/oxl.exe I:/Code R/GarchOxModelling.ox", show.output.on.console = TRUE, wait = TRUE)
But it seams to do nothing. And when i launch manually the file GarchOxModelling.ox, it works.
Would you have any idea on how to make it work from R ?
Thanks in advance
Without testing, try
ret <- system(paste(shQuote("C:/Program Files (x86)/OxMetrics6/ox/bin/oxl.exe"),
shQuote("I:/Code R/GarchOxModelling.ox")),
show.output.on.console = TRUE, wait = TRUE)
A few issues with the code you provided in your question:
It is syntactically wrong R:
"system(C:/Program Fil...", show.output.on.console = TRUE, wait = TRUE)
is like typing in
"ABC", x=1, y=2)
which should error.
Even assuming that the leading quote is not correct, you need to start the quote at the beginning of the executable name, as in
system("C:/Program File...", ...)
Further, though, is that this is being passed verbatim to the shell. While something windows guesses correctly about embedded spaces, it's really not good practice to assume this can happen all of the time, so you should manually quote all of your arguments that either (a) do include a space in them, or (b) you do not know because they are variables. In this case, I prefer shQuote, but dQuote might be sufficient.
system(paste(shQuote("C:/Program Files (x86)/OxMetrics6/ox/bin/oxl.exe"),
shQuote("I:/Code R/GarchOxModelling.ox")),
show.output.on.console = TRUE, wait = TRUE)
I suggest that you consider using intern=TRUE instead of show.output..., so that you can perhaps programmatically verify the output is what you expect.
Last suggestion, I find the processx package much more reliable for calls like this,
# library(processx)
ret <- processx::run("C:/Program Files (x86)/OxMetrics6/ox/bin/oxl.exe", "I:/Code R/GarchOxModelling.ox")
where quoting is handled automatically.
Related
I often run code that eats up a lot of RAM, and may take as much as an hour before it gives its outputs. Often, I'll be half an hour in to running such code and I'll be worrying that something gone wrong. Is there any way that I can get R to reassure me that there's not been any errors yet? I suppose that I could put milestones in to the code itself, but I'm wondering if there's anything in R (or RStudio) that can automatically do this job at run time. For example, it would be handy to see how much memory the code is using, because then I'd be reassured that it's still working whenever I see the memory use significantly vary.
You might like my package {boomer}.
If you rig() your function, all its calls will be exploded and printed as the code is executed.
For instance
# remotes::install_github("moodymudskipper/boomer")
fun <- function(x) {
x <- x + 1
Sys.sleep(3)
x + 1
}
library(boomer)
# rig() the function and all the calls will be exploded
# and displayed as they're run
rig(fun)(2)
One way is:
to make a standalone file containing all the stuff to be run,
sourcing it and getting warned when the code is done, possibly with error.
The small function warn_me below:
runs the source file located in "path"
possibly catches an error, if an error there was
plays a sound when the run is over
sends an email reporting the status of the run: OK or fail
optionally: plays a sound until you stop it, so you can't miss it's over
And here it is:
warn_me = function(path, annoying = FALSE){
# The run
info = try(source(path))
# Sound telling it's over
library(beepr)
beep()
# Send an email with status
library(mailR)
msg = if(inherits(info, "try-error")) "The run failed" else "It's over, all went well"
send.mail(from = "me#somewhere.com",
to = "me#somewhere.com",
subject = msg,
body = "All is in the title.",
smtp = list(host.name = "smtp.mailtrap.io", port = 25,
user.name = "********",
passwd = "******", ssl = TRUE),
authenticate = TRUE,
send = TRUE)
if(annoying){
while(TRUE){
beepr::beep()
Sys.sleep(1)
}
}
}
warn_me(path)
I didn't test the package mailR myself, but any email sending package would do. See this excellent page on sending emails in R for alternatives.
If you are running an R script file within RStudio, use the "Source with Echo" selection (Ctrl+Shift+Enter, or via dropdown).
The system.file commands in my package examples sometimes fail unpredictably, while passing at other times. I do not understand why.
I typically use:
> system.file("examples", "trees.xml", package="RNeXML", mustWork=TRUE)
which usually works, but sometimes fails (even in an interactive session):
Error in system.file("examples", "trees.xml", package = "RNeXML", mustWork = TRUE) :
no file found
when it is failing, I can get this to work:
> system.file("examples", "trees.xml", lib.loc = .libPaths()[1], package="RNeXML", mustWork=TRUE)
[1] "/home/cboettig/R/x86_64-pc-linux-gnu-library/3.0/RNeXML/examples/trees.xml"
Which doesn't make any sense to me, because the documentation of system.file says that it checks libPaths automatically if no value for lib.loc is provided.
So why does it work if I give the .libPaths()[1] explicitly?
It seems like explicitly telling my package to use the first path, .libPaths()[1], would be less stable.
Since this is a heisenbug, set options(error = recover) and when prompted for a frame number, pick the one that brings you into system.file. (For more on what I'm about to explain, see Hadley's Exceptions and Debugging tutorial.) Then step through using the debugger and determine if packagePath gets loaded correctly using find.package(package, lib.loc, quiet = TRUE). I inspected this latter function and couldn't find anything immediately wrong, so it may be something system-specific. Could you post your sessionInfo()?
If packagePath is fine, then the answer lies somewhere in the rest of system.file's body:
FILES <- file.path(packagePath, ...)
present <- file.exists(FILES)
if (any(present))
FILES[present]
else ""
This would make life very hard for us since I doubt there are problems with any of these functions. If packagePath is not what you expect, you can use the recover frame number prompt again to dive back into system.file, and this time type debug(find.package) so you can step through that function. Inspect dirs and paths after the for (lib in lib.loc), and step through the few ifs that follow.
If none of these work, and you don't spot any mischief (which is very hard with the transparency of a step-by-step debugger), you can always try to dump.frames and upload the file for us. I am not sure how useful it will be, since even if we install the same packages, there may be path issues, but it's worth a shot.
Finally, if you don't care about all of the above, a hack that works would be:
trees_path <- ""
for(lib in .libPaths()) {
trees_path <- system.file("examples", "trees.xml", lib.loc = lib, package="RNeXML", mustWork = FALSE)
if (trees_path != "") break;
}
if (trees_path == "") stop("examples/trees.xml not found using any library paths")
I want to create a zip file called "out" not "out.zip". When I run this line:
zip("out", zippedfiles)
where zippedfiles is a list of files, I get out.zip. I am doing this in a Windows environment.
Thanks.
Several people have mentioned that this is the behaviour of zip, but not why this is the cause of what you are seeing. If you look at the source for zip() or even the help ?zip, it should be immediately clear that the behaviour you are seeing comes from the system zip function and nothing to do with R itself. All R does is call the system function for zipping, which by default is zip:
R> zip
function (zipfile, files, flags = "-r9X", extras = "", zip = Sys.getenv("R_ZIPCMD",
"zip"))
{
if (missing(flags) && (!is.character(files) || !length(files)))
stop("'files' must a character vector specifying one or more filepaths")
args <- c(flags, shQuote(path.expand(zipfile)), shQuote(files),
extras)
invisible(system2(zip, args, invisible = TRUE)) ## simply calling system command
}
<bytecode: 0x27faf30>
<environment: namespace:utils>
If you are annoyed by the extension, just issue a file.rename() call after the call to zip():
file.rename("out.zip", "out")
For me, no extension is used if I append . (i.e. a period) to the filename, e.g. out. should work. The full expression: zip("out.", zippedfiles).
For what it's worth, this is due to the default behavior of zip, and is not an issue with R or Windows.
Update 1: In general, it is better to avoid an approach that is OS-specific. I think this approach may create issues if the code is run on other platforms. Gavin's answer, involving renaming, is more portable. What's more, as I suggested in the comments, testing if the target exists using file.exists(), before renaming, adds another layer of safety. An additional layer of safety is obtained by getting a temporary filename via tempfile(). An alternative method of avoiding name collisions when writing or renaming is to use a timestamp in the name.
Is there a way to programmatically find the path of an R script inside the script itself?
I am asking this because I have several scripts that use RGtk2 and load a GUI from a .glade file.
In these scripts I am obliged to put a setwd("path/to/the/script") instruction at the beginning, otherwise the .glade file (which is in the same directory) will not be found.
This is fine, but if I move the script in a different directory or to another computer I have to change the path. I know, it's not a big deal, but it would be nice to have something like:
setwd(getScriptPath())
So, does a similar function exist?
This works for me:
getSrcDirectory(function(x) {x})
This defines an anonymous function (that does nothing) inside the script, and then determines the source directory of that function, which is the directory where the script is.
For RStudio only:
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
This works when Running or Sourceing your file.
Use source("yourfile.R", chdir = T)
Exploit the implicit "--file" argument of Rscript
When calling the script using "Rscript" (Rscript doc) the full path of the script is given as a system parameter. The following function exploits this to extract the script directory:
getScriptPath <- function(){
cmd.args <- commandArgs()
m <- regexpr("(?<=^--file=).+", cmd.args, perl=TRUE)
script.dir <- dirname(regmatches(cmd.args, m))
if(length(script.dir) == 0) stop("can't determine script dir: please call the script with Rscript")
if(length(script.dir) > 1) stop("can't determine script dir: more than one '--file' argument detected")
return(script.dir)
}
If you wrap your code in a package, you can always query parts of the package directory.
Here is an example from the RGtk2 package:
> system.file("ui", "demo.ui", package="RGtk2")
[1] "C:/opt/R/library/RGtk2/ui/demo.ui"
>
You can do the same with a directory inst/glade/ in your sources which will become a directory glade/ in the installed package -- and system.file() will compute the path for you when installed, irrespective of the OS.
This answer works fine to me:
script.dir <- dirname(sys.frame(1)$ofile)
Note: script must be sourced in order to return correct path
I found it in: https://support.rstudio.com/hc/communities/public/questions/200895567-can-user-obtain-the-path-of-current-Project-s-directory-
But I still don´t understand what is sys.frame(1)$ofile. I didn´t find anything about that in R Documentation. Someone can explain it?
#' current script dir
#' #param
#' #return
#' #examples
#' works with source() or in RStudio Run selection
#' #export
z.csd <- function() {
# http://stackoverflow.com/questions/1815606/rscript-determine-path-of-the-executing-script
# must work with source()
if (!is.null(res <- .thisfile_source())) res
else if (!is.null(res <- .thisfile_rscript())) dirname(res)
# http://stackoverflow.com/a/35842176/2292993
# RStudio only, can work without source()
else dirname(rstudioapi::getActiveDocumentContext()$path)
}
# Helper functions
.thisfile_source <- function() {
for (i in -(1:sys.nframe())) {
if (identical(sys.function(i), base::source))
return (normalizePath(sys.frame(i)$ofile))
}
NULL
}
.thisfile_rscript <- function() {
cmdArgs <- commandArgs(trailingOnly = FALSE)
cmdArgsTrailing <- commandArgs(trailingOnly = TRUE)
cmdArgs <- cmdArgs[seq.int(from=1, length.out=length(cmdArgs) - length(cmdArgsTrailing))]
res <- gsub("^(?:--file=(.*)|.*)$", "\\1", cmdArgs)
# If multiple --file arguments are given, R uses the last one
res <- tail(res[res != ""], 1)
if (length(res) > 0)
return (res)
NULL
}
A lot of these solutions are several years old. While some may still work, there are good reasons against utilizing each of them (see linked source below). I have the best solution (also from source): use the here library.
Original example code:
library(ggplot2)
setwd("/Users/jenny/cuddly_broccoli/verbose_funicular/foofy/data")
df <- read.delim("raw_foofy_data.csv")
Revised code
library(ggplot2)
library(here)
df <- read.delim(here("data", "raw_foofy_data.csv"))
This solution is the most dynamic and robust because it works regardless of whether you are using the command line, RStudio, calling from an R script, etc. It is also extremely simple to use and is succinct.
Source: https://www.tidyverse.org/articles/2017/12/workflow-vs-script/
I have found something that works for me.
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
How about using system and shell commands? With the windows one, I think when you open the script in RStudio it sets the current shell directory to the directory of the script. You might have to add cd C:\ e.g or whatever drive you want to search (e.g. shell('dir C:\\*file_name /s', intern = TRUE) - \\ to escape escape character). Will only work for uniquely named files unless you further specify subdirectories (for Linux I started searching from /). In any case, if you know how to find something in the shell, this provides a layout to find it within R and return the directory. Should work whether you are sourcing or running the script but I haven't fully explored the potential bugs.
#Get operating system
OS<-Sys.info()
win<-length(grep("Windows",OS))
lin<-length(grep("Linux",OS))
#Find path of data directory
#Linux Bash Commands
if(lin==1){
file_path<-system("find / -name 'file_name'", intern = TRUE)
data_directory<-gsub('/file_name',"",file_path)
}
#Windows Command Prompt Commands
if(win==1){
file_path<-shell('dir file_name /s', intern = TRUE)
file_path<-file_path[4]
file_path<-gsub(" Directory of ","",file_path)
filepath<-gsub("\\\\","/",file_path)
data_directory<-file_path
}
#Change working directory to location of data and sources
setwd(data_directory)
Thank you for the function, though I had to adjust it a Little as following for me (W10):
#Windows Command Prompt Commands
if(win==1){
file_path<-shell('dir file_name', intern = TRUE)
file_path<-file_path[4]
file_path<-gsub(" Verzeichnis von ","",file_path)
file_path<-chartr("\\","/",file_path)
data_directory<-file_path
}
In my case, I needed a way to copy the executing file to back up the original script together with its outputs. This is relatively important in research. What worked for me while running my script on the command line, was a mixure of other solutions presented here, that looks like this:
library(scriptName)
file_dir <- gsub("\\", "/", fileSnapshot()$path, fixed=TRUE)
file.copy(from = file.path(file_dir, scriptName::current_filename()) ,
to = file.path(new_dir, scriptName::current_filename()))
Alternatively, one can add to the file name the date and our to help in distinguishing that file from the source like this:
file.copy(from = file.path(current_dir, current_filename()) ,
to = file.path(new_dir, subDir, paste0(current_filename(),"_", Sys.time(), ".R")))
None of the solutions given so far work in all circumstances. Worse, many solutions use setwd, and thus break code that expects the working directory to be, well, the working directory — i.e. the code that the user of the code chose (I realise that the question asks about setwd() but this doesn’t change the fact that this is generally a bad idea).
R simply has no built-in way to determine the path of the currently running piece of code.
A clean solution requires a systematic way of managing non-package code. That’s what ‘box’ does. With ‘box’, the directory relative to the currently executing code can be found trivially:
box::file()
However, that isn’t the purpose of ‘box’; it’s just a side-effect of what it actually does: it implements a proper, modern module system for R. This includes organising code in (nested) modules, and hence the ability to load code from modules relative to the currently running code.
To load code with ‘box’ you wouldn’t use e.g. source(file.path(box::file(), 'foo.r')). Instead, you’d use
box::use(./foo)
However, box::file() is still useful for locating data (i.e. OP’s use-case). So, for instance, to locate a file mygui.glade from the current module’s path, you would write.
glade_path = box::file('mygui.glade')
And (as long as you’re using ‘box’ modules) this always works, doesn’t require any hacks, and doesn’t use setwd.
Is there a way to programmatically find the path of an R script inside the script itself?
I am asking this because I have several scripts that use RGtk2 and load a GUI from a .glade file.
In these scripts I am obliged to put a setwd("path/to/the/script") instruction at the beginning, otherwise the .glade file (which is in the same directory) will not be found.
This is fine, but if I move the script in a different directory or to another computer I have to change the path. I know, it's not a big deal, but it would be nice to have something like:
setwd(getScriptPath())
So, does a similar function exist?
This works for me:
getSrcDirectory(function(x) {x})
This defines an anonymous function (that does nothing) inside the script, and then determines the source directory of that function, which is the directory where the script is.
For RStudio only:
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
This works when Running or Sourceing your file.
Use source("yourfile.R", chdir = T)
Exploit the implicit "--file" argument of Rscript
When calling the script using "Rscript" (Rscript doc) the full path of the script is given as a system parameter. The following function exploits this to extract the script directory:
getScriptPath <- function(){
cmd.args <- commandArgs()
m <- regexpr("(?<=^--file=).+", cmd.args, perl=TRUE)
script.dir <- dirname(regmatches(cmd.args, m))
if(length(script.dir) == 0) stop("can't determine script dir: please call the script with Rscript")
if(length(script.dir) > 1) stop("can't determine script dir: more than one '--file' argument detected")
return(script.dir)
}
If you wrap your code in a package, you can always query parts of the package directory.
Here is an example from the RGtk2 package:
> system.file("ui", "demo.ui", package="RGtk2")
[1] "C:/opt/R/library/RGtk2/ui/demo.ui"
>
You can do the same with a directory inst/glade/ in your sources which will become a directory glade/ in the installed package -- and system.file() will compute the path for you when installed, irrespective of the OS.
This answer works fine to me:
script.dir <- dirname(sys.frame(1)$ofile)
Note: script must be sourced in order to return correct path
I found it in: https://support.rstudio.com/hc/communities/public/questions/200895567-can-user-obtain-the-path-of-current-Project-s-directory-
But I still don´t understand what is sys.frame(1)$ofile. I didn´t find anything about that in R Documentation. Someone can explain it?
#' current script dir
#' #param
#' #return
#' #examples
#' works with source() or in RStudio Run selection
#' #export
z.csd <- function() {
# http://stackoverflow.com/questions/1815606/rscript-determine-path-of-the-executing-script
# must work with source()
if (!is.null(res <- .thisfile_source())) res
else if (!is.null(res <- .thisfile_rscript())) dirname(res)
# http://stackoverflow.com/a/35842176/2292993
# RStudio only, can work without source()
else dirname(rstudioapi::getActiveDocumentContext()$path)
}
# Helper functions
.thisfile_source <- function() {
for (i in -(1:sys.nframe())) {
if (identical(sys.function(i), base::source))
return (normalizePath(sys.frame(i)$ofile))
}
NULL
}
.thisfile_rscript <- function() {
cmdArgs <- commandArgs(trailingOnly = FALSE)
cmdArgsTrailing <- commandArgs(trailingOnly = TRUE)
cmdArgs <- cmdArgs[seq.int(from=1, length.out=length(cmdArgs) - length(cmdArgsTrailing))]
res <- gsub("^(?:--file=(.*)|.*)$", "\\1", cmdArgs)
# If multiple --file arguments are given, R uses the last one
res <- tail(res[res != ""], 1)
if (length(res) > 0)
return (res)
NULL
}
A lot of these solutions are several years old. While some may still work, there are good reasons against utilizing each of them (see linked source below). I have the best solution (also from source): use the here library.
Original example code:
library(ggplot2)
setwd("/Users/jenny/cuddly_broccoli/verbose_funicular/foofy/data")
df <- read.delim("raw_foofy_data.csv")
Revised code
library(ggplot2)
library(here)
df <- read.delim(here("data", "raw_foofy_data.csv"))
This solution is the most dynamic and robust because it works regardless of whether you are using the command line, RStudio, calling from an R script, etc. It is also extremely simple to use and is succinct.
Source: https://www.tidyverse.org/articles/2017/12/workflow-vs-script/
I have found something that works for me.
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
How about using system and shell commands? With the windows one, I think when you open the script in RStudio it sets the current shell directory to the directory of the script. You might have to add cd C:\ e.g or whatever drive you want to search (e.g. shell('dir C:\\*file_name /s', intern = TRUE) - \\ to escape escape character). Will only work for uniquely named files unless you further specify subdirectories (for Linux I started searching from /). In any case, if you know how to find something in the shell, this provides a layout to find it within R and return the directory. Should work whether you are sourcing or running the script but I haven't fully explored the potential bugs.
#Get operating system
OS<-Sys.info()
win<-length(grep("Windows",OS))
lin<-length(grep("Linux",OS))
#Find path of data directory
#Linux Bash Commands
if(lin==1){
file_path<-system("find / -name 'file_name'", intern = TRUE)
data_directory<-gsub('/file_name',"",file_path)
}
#Windows Command Prompt Commands
if(win==1){
file_path<-shell('dir file_name /s', intern = TRUE)
file_path<-file_path[4]
file_path<-gsub(" Directory of ","",file_path)
filepath<-gsub("\\\\","/",file_path)
data_directory<-file_path
}
#Change working directory to location of data and sources
setwd(data_directory)
Thank you for the function, though I had to adjust it a Little as following for me (W10):
#Windows Command Prompt Commands
if(win==1){
file_path<-shell('dir file_name', intern = TRUE)
file_path<-file_path[4]
file_path<-gsub(" Verzeichnis von ","",file_path)
file_path<-chartr("\\","/",file_path)
data_directory<-file_path
}
In my case, I needed a way to copy the executing file to back up the original script together with its outputs. This is relatively important in research. What worked for me while running my script on the command line, was a mixure of other solutions presented here, that looks like this:
library(scriptName)
file_dir <- gsub("\\", "/", fileSnapshot()$path, fixed=TRUE)
file.copy(from = file.path(file_dir, scriptName::current_filename()) ,
to = file.path(new_dir, scriptName::current_filename()))
Alternatively, one can add to the file name the date and our to help in distinguishing that file from the source like this:
file.copy(from = file.path(current_dir, current_filename()) ,
to = file.path(new_dir, subDir, paste0(current_filename(),"_", Sys.time(), ".R")))
None of the solutions given so far work in all circumstances. Worse, many solutions use setwd, and thus break code that expects the working directory to be, well, the working directory — i.e. the code that the user of the code chose (I realise that the question asks about setwd() but this doesn’t change the fact that this is generally a bad idea).
R simply has no built-in way to determine the path of the currently running piece of code.
A clean solution requires a systematic way of managing non-package code. That’s what ‘box’ does. With ‘box’, the directory relative to the currently executing code can be found trivially:
box::file()
However, that isn’t the purpose of ‘box’; it’s just a side-effect of what it actually does: it implements a proper, modern module system for R. This includes organising code in (nested) modules, and hence the ability to load code from modules relative to the currently running code.
To load code with ‘box’ you wouldn’t use e.g. source(file.path(box::file(), 'foo.r')). Instead, you’d use
box::use(./foo)
However, box::file() is still useful for locating data (i.e. OP’s use-case). So, for instance, to locate a file mygui.glade from the current module’s path, you would write.
glade_path = box::file('mygui.glade')
And (as long as you’re using ‘box’ modules) this always works, doesn’t require any hacks, and doesn’t use setwd.