I would like to use on a batch file a directory path that will change from people to people (it is inside a shared folder) and need to access a grand parent folder.
Right now I have the following:
"%CD%\R\R-3.4.2\bin\i386\R.exe" CMD BATCH "%CD%\run.R"
this works when R folder is on the same level as run.R file. But now I want to use the following structure:
-R
-dashboards/folder1/run.R
ie, R folder and dashboards folder are on the same level, and run.R is two levels below inside dashboards folder.
I'm asking for help to wright the correct directory to my R folder on the batch file.
Thanks in advance
If you put the code at the end of this answer in a Windows batch file it will run run.R provided that
run.R is in the current directory and
R is referenced in the registry (which would be the case for a default R install)
Optionally the user can specify the location of R by defining the R_HOME batch variable to point to the current version of R
set R_HOME=C:\Program Files\R\R-3.4.1
... now run batch file ...
They might want to do that if R is not in the registry or if they have multiple versions of R and don't want to use the currently registered one. In the usual case that would not be necessary.
This effectively decouples the location of R and the location of run.R allowing it to be placed anywhere independently of the location of R.
#echo off
setlocal
if not defined R_HOME for /f "tokens=2*" %%a in (
'reg query hklm\software\wow6432Node\r-core\r /v InstallPath 2^>NUL ^| findstr InstallPath'
) do set R_HOME=%%~b
"%R_HOME%\bin\R" BATCH run.R
Related
I am trying to add my R script into a dockerfile. The beginning of the file (loading base image, installing necessary packages) works fine when I run it in my terminal, but I keep getting this error when it gets to the line that contains the R script I want to run:
Step 15/17 : COPY /Users/emma/Documents/folder1/examples/question-1/model-1.r .
COPY failed: stat /var/lib/docker/tmp/docker-builder376572603/Users/emma/Documents/folder1/examples/question-1/model-1.r: no such file or directory
I am already running the terminal out of the "question-1" directory (my shell command looks like this) :
Emmas-MacBook-Air-2:question-1 emma$
and the R script file "model-1.r" is in that folder. What am I doing wrong in detailing the path to the R script? Do I have to somehow transform the script before adding it to the dockerfile?
Thank you
I believe, that you have to specify relative (to your build folder) path to copy from. Source:
Multiple resources may be specified but the paths of files and directories will be interpreted as relative to the source of the context of the build.
And file to copy should be inside context of the build. So if your Dockerfile is located in folder A, then the objects you would like to copy should be placed in the folder A or it's subfolders.
I have a series of pieces of R code which have been designed to be run on other computers. That is, all code is relative to a root directory, which contains a Rstudio project file, .Rproj. There are no absolute file paths. This works fine when I actually open Rstudio, load the .Rproj file and then run the code.
However some of my code takes hours to run, and I need to set multiple scripts to run one after the other. This means creating a .sh file, and running the R script in turn from the command line. However non of my programs run successfully from the command line, as the root directory is no longer set to that of the .Rproj file. I have read about the here package can be used, which will automatically set the root directory to where ever a .here file is located. This is not the case for me.
The working directory it automatically uses is the home directory I have on the computational cluster I am using. The area where all my files, including the .Rproj and .here files is located in a different directory in which I have a lot more space allocated. Both are accessible from a common parent directory, so I assumed there here() function would be able to locate the directory I want to actually use to run my work. But this is not the case.
Effectively, I would like to set the root directory to a location which is not the default root directory on the system I am using. I have put a .here file there, but this is not located by there here() function, which I believe is its primary objective. Any ideas on how to proceed?
EDIT: I am working on a UNIX system. R version 3.4.2.
My problem was similar, but not exactly the same as yours. Perhaps my solution will work for you. When I opened an RStudio project, I found that if I called "library(here)", the root directory is set where the .Rproj file is located and that "set_here" would not change that directory, despite the 'here' package documentation. Perhaps I was doing something wrong, but I decided to solve the problem with a simple R function that moves up the directory tree until it finds a ".here" file. It then loads the "here" package and that sets the root directory where I want it.
I use "touch .here" in a Terminal outside of R to set my root directory, and then call "init_here()" from my newly opened R project:
init_here <- function() {
`%!in%` = Negate(`%in%`)
files <- dir( all.files = T )
while ( ".here" %!in% files & getwd()!="/" ) {
setwd("..")
files <- dir( all.files = T )
}
library(here)
}
Use Case -
In Unix:
cd( '~/myRoot' )
touch( '.here' )
In RStudio, when I open a project, the calls look like:
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
< R information removed for clarity >
[Workspace loaded from ~/myRoot/myProject/.RData]
> getwd()
[1] "/Users/me/myRoot/myProject"
> init_here()
here() starts at /Users/me/myRoot
> here()
[1] "/Users/me/myRoot"
>
I can now put a ".here" file at the root of each of my RStudio projects and set the expected root directory independently for each project. If you want to get fancy, you could put the function in each project's .Rprofile so that it runs whenever the project is opened. All of my projects have the .Rproj file in the directory above my "R" directory, so my .Rprofile looks like:
source("./R/init_here.R")
init_here()
Hope that helps.
Did you try simply adding a cd /the/path/where/you/put/the/files command in your shell script?
According to this documentation, here() "uses a reasonable heuristics to find your project's files, based on the current working directory at the time when the package is loaded". The "cd" (change directory) command in a shell script changes the current working directory.
The File below:
; Install common files
SetOutPath "${GameDir}\Mopy"
File /r /x "*.bat" /x "*.py*" /x "w9xpopen.exe" /x "Wrye Bash.exe" "Mopy\*.*"
filters out some directories that contain python files but still those directories are created (although empty, or containing empty subdirectories) when I run the installer. Those folders need to be included to the installer (if I get the terminology correct at "compile time") cause the installer has an option to install the python version of the program. I can't come up with a way to not add these empty folders. Is there some wildcard I could use to that purpose or should I go and remove the files on installation (using RMDir ?) ?
I'd say you have two options and one is indeed RMDir if you are OK with it possibly removing empty folders that the user created.
The other option is to not use File /r ... and instead use !system to execute something like a batch file that generates a text file with individual File instructions that you can !include. It would look something like this:
!tempfile files
!system '"mygeneratefilelist.bat" "${files}"'
!include "${files}"
!delfile "${files}"
and the batch file would use FOR and/or DIR to list and ECHO the File commands to %1...
I was using R installed on a Linux server using SSH. Everything was fine, but now I have been denied access to temp folder and if I am loading R it is giving error cannot create 'R_TempDir', as it can't create the temp folder.
Can you please tell me how to create own local temp folder so that R can create temporary directory there ?
You can try to set one of these environment variable :
TMPDIR, TMP, TEMP:
Consulted (in that order) when setting the temporary directory for the session: see tempdir. TMPDIR is also used by some of the utilities see the help for build
by doing for instance :
export TMPDIR=/tmp
source
Hope this answers.
From what I understand,
I just thought that you could use .bashrc files in your /home/username/ directory
~# nano /home/username/.bashrc
You can put the command to create the folder inside this .bashrc file by just adding this line mkdir /your/dir/path/yourDir
This file is just like an autorun file which run everytime you upstart your linux server
But this is just working per user setting
I want to change the prompt in R from > to R> and I know I should use the options command options(prompt="...") and it works, but then when I restart R the prompt is back to >.
Is there anyway to save the change so that it sticks?
Use .Rprofile file:
You can customize the R environment through a site initialization file or a directory initialization file. R will always source the Rprofile.site file first. On Windows, the file is in the C:\Program Files\R\R-n.n.n\etc directory. You can also place a .Rprofile file in any directory that you are going to run R from or in the user home directory.
At startup, R will source the Rprofile.site file. It will then look for a .Rprofile file to source in the current working directory. If it doesn't find it, it will look for one in the user's home directory. There are two special functions you can place in these files. .First( ) will be run at the start of the R session and .Last( ) will be run at the end of the session.
More details are here