I'm trying to get an R script to run from a batch file so it can be nice and clean for other users. Currently, you drag and drop a CSV file onto the batch file and it passes the file name to the R script for input.
When there's a space in the file path/name it works fine in RStudio but causes problems when I call it from the batch file. When I do that it tries to open the path before the space.
I've tried to reformat the file path from within R by using shortPathName(inputPath) and by replacing spaces with "\ " but it doesn't seem to work.
At the moment, the script is launched with
"%~dp0\R-3.6.0\bin\R.exe" CMD BATCH "--args %~1" "%~dp0\Script.R"
with the script containing
args <- commandArgs(TRUE)
inputPath <- args[1]
inputPath <- shortPathName(inputPath)
inputData <- read.csv(inputPath)
It runs fine from within RStudio but crashes when launched from the batch producing this error message in the output file:
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'file path up to the space': No such file or directory
Execution halted
By no means a R expert, but I'd try
%~dp0\R-3.6.0\bin\R.exe" CMD BATCH "--args %~s1" "%~dp0\Script.R"
The %~s1 should supply the short filename as the argument.
After trying several formulations of the batch file and some debugging, I found that the batch file was passing the first part of the file before the space as the first argument.
After finding that the use of R in CMD BATCH mode is no longer advisable so switched to running using Rscript mode as
"%~dp0\R-3.6.0\bin\Rscript.exe" --vanilla "%~dp0\Script.R" "%~1"
This allowed for the argument to be passed to R with "", and hence with the space.
Since v3.5.1, R accepts file paths with spaces.
Related
I am trying to download and unzip a folder of files from GitHub into R. I can manually download the file at https://github.com/dylangomes/SO/blob/main/Shape.zip and then extract all files in working directory, but I'd like to work directly from R.
utils::unzip("https://github.com/dylangomes/SO/blob/main/Shape.zip")
# Warning message:
# In utils::unzip("https://github.com/dylangomes/SO/blob/main/Shape.zip", :
# error 1 in extracting from zip file
It says it is a warning message, although nothing has been downloaded or unzipped into my wd.
I can download the file to my machine:
utils::download.file("https://github.com/dylangomes/SO/blob/main/Shape.zip")
But I get the same message with the unzip function:
utils::unzip("Shape.zip")
And the downloaded file cannot manually be extracted. Here, I get the error that the compressed folder is empty. The unzip line works on the manually downloaded .zip file, which tells me something is wrong with the download.file line.
So if I add raw=TRUE to the end (which can make a difference in downloading data from GitHub):
utils::download.file("https://github.com/dylangomes/SO/blob/main/Shape.zip?raw=TRUE","Shape.zip")
utils::unzip("Shape.zip")
I get a different warning with, similarly, nothing being executed:
Warning message:
In utils::unzip("Shape.zip") : internal error in 'unz' code
I have tried most of the answers at Using R to download zipped data file, extract, and import data, but they appear to be for single files that are zipped and aren't helping here. I've tried the answers at r function unzip error 1 in extracting from zip file, which mentions the same warning message I am getting, but none of the solutions work in this case.
Any idea of what I am doing wrong?
You need to use:
download.file(
"https://github.com/dylangomes/SO/blob/main/Shape.zip?raw=TRUE",
"Shape.zip",
mode = "wb"
)
Without the query string ?raw=TRUE you are downloading the webpage and not the file.
(For Windows) R will use mode = "wb" by default when it detects from the end of the URL that certain file formats, including .zip, are being downloaded. However, the URL finishing with a query string instead of a file format means the check fails so you need to set the mode explicitly.
I'm having issues reading the data on the desktop version of Rstudio on mac. When I do the usual read.csv it shows the error shown in the title. This is the first time this has happened. I have tried to change my working directory in 'Sessions' at the top and also to read the file with its granularity
You could try rstudioapi library to set an unique wd for your script path and then use read.csv() where path= "test.csv"
library(rstudioapi)
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))
Test <- read.csv("test.csv")
I want to open a file from within R.
I can launch the software (graphpad prism) with the following:
system2("C:/Program Files (x86)/GraphPad/Prism 7/prism.exe")
I expected this to open my prism file as if I were double clicking on it or running it from cmd, but it didn't:
system2("H:/Graphs/Shell/Templates/NASH4_Standard.pzfx")
I am receiving the message:
Warning message: running command
'H:/Graphs/Shell/Templates/NASH4_Standard.pzfx' had status 127
I see that this is not an error but just a warning. Am I unintentionally "shelling" the document in the background? How would I make sure it pops up as a window?
Status 127 was addressed here, but for launching the software, not opening the document with it.
In Windows environments, you need to call a command line interpreter like CMD prompt or PowerShell. Also, any file path that has spaces needs to be enclosed in double quotes above the quotes needed in R for string literals (the case for your .exe not specific file).
With system() send entire command in one string:
system('cmd /c "H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"')
# POWER SHELL REQUIRES MORE QUOTE ESCAPING (ONLY ONE PAIR W/O SPACES)
system('powershell & """H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"""')
With system2() use the args parameter:
# FILES
system2('cmd', args=c('/c', '"H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"'))
system2('powershell', args=c(' & """H:/Graphs/Shell/Templates/NASH4_Standard.pzfx"""'))
# EXECUTABLES
system2('cmd', args=c('/c', '"C:/Program Files (x86)/GraphPad/Prism 7/prism.exe"'))
system2('powershell', args=c(' & """C:/Program Files (x86)/GraphPad/Prism 7/prism.exe"""'))
shell.exec("C:/Program Files (x86)/GraphPad/Prism 7/prism.exe")
does it work for you ?
ps. and shell.exec("MyWorkbook.xls") open file with default program
I have a xlsx file and to read from Rstudio i saved it as .csv file. Now when i try to read the file from Rstudio, receiving the below error.
setwd("D:/DATA SCIENCE/CCPP-Linear regression")
ccpp<- read.csv("Folds5x2_pp.csv", header = TRUE)
Error in file(file, "rt") : cannot open the connection In addition:
Warning message: In file(file, "rt") : cannot open file
'Folds5x2_pp.csv': No such file or directory
As already mentioned in the comments, the "cannot open the connection" part of the error message confirms that where R is looking is not where the file is.
A few things to keep in mind
use getwd() to see the current R working directory
use setwd() to change R's wd
You should use RStudio projects to organize your projects - this helps with the working directory thing
spaces in paths are difficult sometimes. Looks like you have "D:/DATA SCIENCE", that space can cause problems (you may need to escape the space like "DATA\ SCIENCE".
You can read the file using the full path (e.g. read.csv("D:/DATA SCIENCE/path/file.csv")) or if you are doing this a lot, set a variable to your path data_path ="D:/DATA SCIENCE/path/" and then read.csv(file.path(data_path, "file.csv")) where file.path concatenates with your OS specific path delimiter.
You can import files into RStudio using the Import Dataset option under Tools in the menu bar.
I am trying to trigger a FORTRAN code from R.
For that I am creating a .so file by giving command
R CMD SHLIB filename.f
The .so file is created without any warnings(!!)
To lead the file in R, I give the following command in R
dyn.load("filename.so")
The file gets loaded as it shows when I give command getLoadedDlls() in R.
But when I try to run it using .Fortran("filename") it throws an error
Error in .Fortran("filename") : Fortran symbol name "filename" not in
load table