I am using the testthat package in R and I am trying to test a function
defined in a file example.R. This file contains a call source("../utilities/utilities.R") where utilities.R is a file with functions written by me. However, when I am trying to test a function from example.R, sourcing it within the testing script gives the following error:
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
cannot open file '../utilities/utilities.R': No such file or directory
Could you please clarify how to run tests for functions in files that source another file?
Might be a bit late, but I found a solution. Test_that sets the directory holding the test file as the current working directory. See the code below from test-files.r. This causes the working directory to be /tests. Therefore, your main scripts need to source ("../file.R"), which works for testing, but not for running your app.
https://github.com/hadley/testthat/blob/master/R/test-files.r
source_dir <- function(path, pattern = "\\.[rR]$", env = test_env(),
chdir = TRUE) {
files <- normalizePath(sort(dir(path, pattern, full.names = TRUE)))
if (chdir) {
old <- setwd(path)
on.exit(setwd(old))
}
The solution I found was to add setwd("..") in my test files and simply source the file name without the path. source("file.R") instead of source("../file.R"). Seems to work for me.
testthat allows you to define and source helper files (see ?source_test_helpers):
Helper scripts are R scripts accompanying test scripts but prefixed by helper. These scripts are run once before the tests are run.
So what worked perfectly for me is simply putting a file "helper-functions.R" containing the code that I want to source in "/tests/testthat/". You don't have to call source_test_helpers() yourself, testthat will automatically do that when you run tests (e.g., via devtools::test() or testthat::test_dir()).
No great solution to this problem I've found, so far mine has been to set the working directory within each test using the package here.
test_that('working directory is set',{
setwd(here())
# test code here
})
I put the source("C:/Users/.../Utilities.R") in the test file.
Related
## this script assumes that it is started in the working directory
tracker_directory<-normalizePath(getwd())
# setting parameters ------------------------------------------------------
# additional R configuration ----------------------------------------------
# load packages
library(magrittr)
setwd(dirname(getwd()))
# load helper functions
source("R/max_departure.r")
# run methodologies -------------------------------------------------------
Here I have the R file which is referencing to other R file
[1]: https://i.stack.imgur.com/s9Mm3.png
Note that dirname(getwd()) returns the parent directory of your current working directory. Maybe that is the issue? If getwd() returns the directory that contains main.R there is no need for the setwd() call, I think.
I am creating a series of r scripts that will be used by multiple people, meaning that the working directory of files used and stored will differ. There are two folders, one for the R code, called "rcode," and another to store the generated outputs, called "data". These two folders will always be shared in tandem. To accommodate for the changing working directory I created a "global" script that has the following lines of code and resides in the "rcode" folder:
source_path = rstudioapi::getActiveDocumentContext()$path
setwd(dirname(source_path))
swd_data <- paste0("..\\data\\")
The first line gets the source path of the global script. The second line makes this the working directory. The third line essentially tells the script to store an output in the "data" folder, which has the same path as the "rcode" folder. So to read in a csv file within the "data" folder I write:
old_total_demand <- read.csv(paste0(swd_data, "boerne_total_demand.csv"))
When I use this script on my Windows laptop it works beautifully, but when I use it on my Mac I get the following error:
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '..\data\demand\boerne_total_demand.csv': No such file or directory
Would anyone have any idea why this would be? Thanks in advance for the help.
I'm not sure what systems your collaborators will be using, but you may run into issues due to differences between Window/Mac/Linux with regards to how paths are written. I suggest you create a R Project .Rprj using RStudio and save that in your directory that contains subdirectories for data and rcode, and share the entire project directory.
/Project_dir/MyProject.Rprj
/Project_dir/data/
/Project_dir/rcode/
Then from the R project opened through RStudio you should be able to directly refer to your data by:
data <- read.csv("data/boerne_total_demand.csv")
The working directory will always be where your .Rproj is stored, so you can avoid having to setwd as it causes lots of chaos when sharing and collaborating with others.
I have this code from my current script at hand.
I hope you like it !
path <- dirname(getActiveDocumentContext()$path)
setwd(path)
swd_path <- paste0(path,"/data/")
if(!dir.exists(swd_path)){
dir.create(swd_path)
}
old_total_demand <- read.csv(paste0(swd_data, "boerne_total_demand.csv"))
I installed R and RStudio this week on a new Windows 10 machine. I want to use this R code to launch Excel and open a CSV file that is in a subdirectory of the current working directory:
file <- "example.csv"
sub_dir <- "subdirectory"
shell.exec(file.path(sub_dir, file))
But I get this error:
Error in shell.exec(file.path(sub_dir, file)) :
'subdirectory/example.csv' not found
However, if I provide shell.exec with the full file path, this code works as expected:
shell.exec(file.path(getwd(), sub_dir, file))
The documentation for shell.exec states:
The path in file is interpreted relative to the current working
directory.
R versions 2.13.0 and earlier interpreted file relative to the R home
directory, so a complete path was usually needed.
Why doesn't my original code (without getwd) not work? Thanks.
It looks to be related to the path separator in some wacky way. Below, I specify the the file path separator as \ and the command executes as expected. You could keep your call to file.path() and simply wrap in normalizePath() as another option.
file <- "example.csv"
sub_dir <- "subdirectory"
dir.create(sub_dir)
writeLines("myfile",file.path(sub_dir, file))
# Works
shell.exec(file.path(sub_dir, file, fsep = "\\"))
shell.exec(file.path(sub_dir, file))
#> Error in shell.exec(file.path(sub_dir, file)): 'subdirectory/example.csv' not found
This may be a duplicate, but I couldn't find a solution when I searched online and it's an issue that has been bugging me for some time. I am given a zip file with 2 .R files, I download the zip and move the .R files into a directory on my computer, let's say "/Users/Home/StatisticsStuff/LearningR/".
My two files are Stats1.R and Stats2.R, and the first line of code in Stats1.R is:
source(Stats2.R)
and I get the following error message:
> source("Stats2.R")
Error in file(filename, "r", encoding = encoding) : cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) : cannot open file 'Stats2.R': No such file or directory
when i run getwd(), to see which working directory I'm in, I get:
getwd()
"/Users/Home"
It seems like it would be a pain to have to change working directories in order to source files? Is there something I'm doing wrong here with regards to what I'm expecting from the source() function? Do I have to put a line in my code above everything else using setwd("whatever the correct wd is").
Any thoughts appreciated!
I added this before sourcing, it worked for me :
setwd(dirname(getwd()))
first write this command list.files() then you can know which location of your R is pointing or see the below image that R-Pointing to then write the source command with correct path. it will be executed.
follow these steps to see the R pointing path.
Go to properties of your R software which is installed as below
Find the Start in path: which is the path R pointing to so in source command use that path
I want to deploy a basic trained R model as a webservice to AzureML. Similar to what is done here:
http://www.r-bloggers.com/deploying-a-car-price-model-using-r-and-azureml/
Since that post the publishWebService function in the R AzureML package was has changed it now requires me to have a workspace object as first parameter thus my R code looks as follows:
library(MASS)
library(AzureML)
PredictionModel = lm( medv ~ lstat , data = Boston )
PricePredFunktion = function(percent)
{return(predict(PredictionModel, data.frame(lstat =percent)))}
myWsID = "<my Workspace ID>"
myAuth = "<my Authorization code"
ws = workspace(myWsID, myAuth, api_endpoint = "https://studio.azureml.net/", .validate = TRUE)
# publish the R function to AzureML
PricePredService = publishWebService(
ws,
"PricePredFunktion",
"PricePredOnline",
list("lstat" = "float"),
list("mdev" = "float"),
myWsID,
myAuth
)
But every time I execute the code I get the following error:
Error in publishWebService(ws, "PricePredFunktion", "PricePredOnline", :
Requires external zip utility. Please install zip, ensure it's on your path and try again.
I tried installing programs that handle zip files (like 7zip) on my machine as well as calling the utils library in R which allows R to directly interact with zip files. But I couldn't get rid of the error.
I also found the R package code that is throwing the error, it is on line 154 on this page:
https://github.com/RevolutionAnalytics/AzureML/blob/master/R/internal.R
but it didn't help me in figuring out what to do.
Thanks in advance for any Help!
The Azure Machine Learning API requires the payload to be zipped, which is why the package insists on the zip utility being installed. (This is an unfortunate situation, and hopefully we can find a way in future to include a zip with the package.)
It is unlikely that you will ever encounter this situation on Linux, since most (all?) Linux distributions includes a zip utility.
Thus, on Windows, you have to do the following procedure once:
Install a zip utility (RTools has one and this works)
Ensure the zip is on your path
Restart R – this is important, otherwise R will not recognize the changed path
Upon completion, the litmus test is if R can see your zip. To do this, try:
Sys.which("zip")
You should get a result similar to this:
zip
"C:\\Rtools\\R-3.1\\bin\\zip.exe"
In other words, R should recognize the installation path.
On previous occasions when people told me this didn’t work, it was always because they thought they had a zip in the path, but it turned out they didn’t.
One last comment: installing 7zip may not work. The reason is that 7zip contains a utility called 7zip, but R will only look for a utility called zip.
I saw this link earlier but the additional clarification which made my code not work was
1. Address and Path of Rtools was not as straigt forward
2. You need to Reboot R
With regards to the address - always look where it was installed . I also used this code to set the path and ALWAYS ADD ZIP at the end
##Rtools.bin="C:\\Users\\User_2\\R-Portable\\Rtools\\bin"
Rtools.bin="C:\\Rtools\\bin\\zip"
sys.path = Sys.getenv("PATH")
if (Sys.which("zip") == "" ) {
system(paste("setx PATH \"", Rtools.bin, ";", sys.path, "\"", sep = ""))
}
Sys.which("zip")
you should get a return of
" C:\\RTools|\bin\zip"
From looking at Andrie's comment here: https://github.com/RevolutionAnalytics/AzureML/commit/9cf2c5c59f1f82b874dc7fdb1f9439b11ab60f40
Implies we can just download RTools and be done with it.
Download RTools from:
https://cran.r-project.org/bin/windows/Rtools/
During installation select the check box to modify the PATH
At first it didn't work. I then tried R32bit, and that seemed to work. Then R64 bit started working again. Honestly, not sure if I did something in the middle to make it work. Only takes a few minutes so worth a punt.
Try the following
-Download the Rtools file which usually contains the zip utility.
-Copy all the files in the "bin" folder of "Rtools"
-Paste them in "~/RStudio/bin/x64" folder