.RData files are starting to invade my directory structure. I would like to retain a single one in a specified directory. Is there such an ENV variable similar to R_HISTFILE?
This is in reference to the default save/restore directory for R workspaces.
UPDATE The answer by JThorpe led to the following solution:
set Env var RPROFILE_USER to a desired location . I am using my home dir
i.e.:
export RPROFILE_USER=/Users/steve
In that directory create a file with setwd (set working directory)
i.e:
$cat ~/.Rprofile
setwd('/Users/steve')
Now the .RData will always load/save to the home dir (or whatever dir you put in setwd)
I personally dislike having R retain anything between sessions b/c it makes for difficult to find errors owing to variables that persist between sessions. Hence I set the “no-save” and “no-restore” options so that R neither writes its current state to an .Rdata file nor attempts to read in an old state. If I do happen to want to save an R session (this happens VERY rarely) I call savehistory().
Methods for setting command line options in OSX can be found here, and what follows describes setting command line options for R (or any other program) in windows.
To set the no-save and no-restore options in Windows, right-click on the R icon that you use to start an R session and select the ‘properties’ option. In the properties box, the “target” string should look something like this:
“C:\Program Files\R\R-3.1.2\bin\i386\Rgui.exe”
To this string, add this string ‘ --no-save --no-restore’. Note that there is a space before each of the double-dashes. The target should now look something like this:
“C:\Program Files\R\R-3.1.2\bin\i386\Rgui.exe” --no-save --no-restore
Click ‘Ok’ or ‘Apply’ to save these options. Note that these are per-icon (shortcut) settings. I have several icons with different command line options depending on the setting I want in the R session. Additional command line arguments to R can be found here.
Try the Load command in the Hmisc package. It uses the LoadPath option for this.
If you create a .Rprofile file you can specify a default working directory. See ?Startup for more details including the ability to set a site-wide profile. I just referred to that help page to make sure the .RData would be affected by that setting.
Related
I am using bash on Linux Centos. I set up the R_LIBS_USER from my $HOME/.bashrc. Also tried to set this up on $HOME/.Renviron
# in .bashrc
export R_LIBS_USER=$HOME/lib/R/site-library
cat .Renviron
R_LIBS_USER=$HOME/lib/R/site-library
I made sure R_LIBS_USER is set up properly. Echo show the proper value. However running R from this terminal that gives the proper value of R_LIBS_USER does not pick up this value.
> .libPaths()
[1] "/global/software/r/3.5.0/lib64/R/library"
The .libPaths() only shows the default library path in stead of my personal one. $HOME/lib/R/site-library is not in the output of .libPaths(). When I tried to load libraries inside $HOME/lib/site-library I got package not found error. I can add the personal path from inside R, then I can load libraries inside my personal R lib directory.
> .libPaths(c("/myhome/lib/R/site-library", .libPaths()))
> .libPaths()
[1] "/myhome/lib/R/site-library"
[2] "/global/software/r/3.5.0/lib64/R/library"
I have searched for two days to look for a solution. Other people had similar problems and also had no solutions. I used to be able to pick up the personal library path, but don't know what I changed that abolished this normal behavior.
Finally figured it out, .Renviron file does not do expansion of variable $HOME, not like those in .bashrc. R_LIBS_USER variable will be set to $HOME/lib/R/site-library. This is an invalid path when $HOME is not expanded. R will not tell you that this is wrong. Just silently move on to its normal business (I think this is a design flaw in R, no exception handling).
.libPaths("/nonexistent/path") # has no effect on the result of .libPaths()
# except that it will maintain the default R library and remove any exisiting
# personal library. And will not tell you anything wrong with the nonexistent
# directory
Before the .libPath("/nonexistent/path") call, I had two elements in the vector: one /default/R/library, ether other /my/persoanl/R/lib after the assignment only the former is left. R is full of surprises.
Close and valid solution ... but you can try one more thing here to improve ... since you then would not need to maintain things in multiple places ie you can reuse your exported environment variables in .Renviron
You should be able to achieve that if you replace
R_LIBS_USER=$HOME/lib/R/site-library
with
R_LIBS_USER="${HOME}/lib/R/site-library"
the "${...}/..." (so { brackets around the variable and whole path or expression enclosed in double or single quotes) will/should make the path expansion from .Renviron succeed.
I'm using a Mac. The path.expand function is several folders removed from my desired working directory. For example:
path.expand('~')
[1] "/Users/my.name"
I'd like to change it to something like this:
path.expand('~')
[1] "/Users/my.name/drive/R/project/sub.folder"
How can I go about this?
Thank you.
The tilde is, in all unix-sen (including macos), special in that it refers to what the operating system considers the home directory (via the env var HOME).
There are two types of answers to this. Can it be done? Perhaps, sure even. Should it be done? There will likely be unintended consequences (that may be hard to troubleshoot and/or workaround), so likely not.
This works on my ubuntu box:
me#mybox:/some/path$ Rscript -e 'Sys.getenv("HOME")'
[1] "/home/me"
me#mybox:/some/path$ HOME=/tmp/ Rscript -e 'Sys.getenv("HOME")'
[1] "/tmp/"
me#mybox:/some/path$ Rscript -e 'Sys.setenv(HOME="/tmp/");Sys.getenv("HOME")'
[1] "/tmp/"
(This notably does not work as well on Windows ... which is not very unix-y of it!)
So you can try overriding it with either:
Sys.setenv(HOME = "/Users/my.name/drive/R/project/sub.folder"), or
Set the HOME variable in your working environment before starting R.
This might have unintended consequences. For instance, R looks for ~/.Rprofile, and git and commands look for ~/.gitconfig and such.
My recommended way-ahead would be to define a variable and change there. If you use RStudio, then its "Projects" can always start you in the correct directory. If not and you still want this "special directory" available to you, perhaps add this to your /Users/username/.Rprofile (in your "actual" homedir)
.specialdir <- "/Users/my.name/drive/R/project/sub.folder"
and, whenever you need to go there, use file.expand(.specialdir). One side-effect of this is that any of your code, functions, reports, whatever that use this will no longer be reproducible.
A way to easily reference your files without needing to change the HOME directory is to use the here package. This basically uses a heuristic to find the right working directory based on where your script is. Normally it looks for RStudio Project files (.rproj) or for a .git file if your working directory is a git repository. It's easy to use and robust to moving machines or accidental use of setwd, or even forgetting to set HOME on a different machine/profile.
If your data file some_data.csv above is stored in /Users/my.name/drive/R/project/sub.folder/some_data.csv, where project is the root folder for the project:
here::here()
[1] "/Users/my.name/drive/R/project"
here::here("sub.folder", "some_data.csv")
[1] "/Users/my.name/drive/R/project/sub.folder/some_data.csv"
and you can use it as a drop in replacement for the path, as in:
data <- read_csv(here::here("sub.folder", "some_data.csv"))
I used to have it set up that R commander plug-in would start up automatically every time I opened the R application, but I've upgraded R and can't remember how I did it.
Here is Scott Hyde's instructions for creating a shortcut to start R commander every time you start R.
Open up the C:\Program Files\R\R-2.10.1\etc (or similarly named version directory).
Edit the file Rprofile.site and add the following lines. The mylibs variable is a list of packages that you want starting up each time you run Rcmdr. Both lattice and MASS are depencies of Rcmdr and need to be loaded. If you load them this way, they are loaded SILENTLY!
defpack = getOption("defaultPackages")
mylibs = c("tcltk","car","lattice","MASS","Matrix")
if(Sys.getenv("RCMDR") == "TRUE") mylibs = c(mylibs,"Rcmdr")
options(defaultPackages = c(defpack,mylibs))
Next, copy the shortcut that is used to run R onto the Desktop. Right click on the file, and select properties Add the following to the end of the "Target:"
"C:\Program Files\R\R-2.10.1\bin\Rgui.exe" --sdi RCMDR=TRUE
Notice that the options are OUTSIDE of the quotation marks.
Change the name of the shortcut you just made to "Rcmdr"
Double click on it, and both R and Rcmdr start!
Recently started using R, and I was testing out the other solution given by #user123943, and it just couldn't seem to work out right. Thought maybe there'd be a simpler solution and tried it and it worked fine. All you need to do is:
Find the Rprofile.site file (it should be in an etc file somewhere inside your R program file) (e.g.: C:\Program Files\R\R-4.1.1\etc)
Edit the file (give yourself permissions to edit if required) by adding in library(Rcmdr) at the end of the file.
That's it! Quick and easy solution! If you decide to revert it back all you will need to do is remove the added code at the end of the Rprofile.site file :)
Of course, save the file before opening up R again!
How can a sourced or Sweaved file find out its own path?
Background:
I work a lot with .R scripts or .Rnw files.
My projects are organized in a directory structure, but the path of the project's base directory frequently varies between different computers (e.g. because I just do parts of data analysis for someone else, and their directory structure is different from mine: I have projects base directories ~/Projects/StudentName/ or ~/Projects/Studentname/Projectname and most students who have just their one Project usually have it under ~/Measurements/ or ~/DataAnalysis/ or something the like - which wouldn't work for me).
So a line like
setwd (my.own.path ())
would be incredibly useful as it would allow to ensure the working directory is the base path of the project regardless of where that project actually is. Without the need that the user must think of setting the working directory.
Let me clarify: I look for a solution that works with pressing the editor's/IDE's source or Sweave Keyboard shortcut of the unthinking user.
Just FYI, knitr will setwd() to the dir of the input file when (and only when) evaluating the code chunks, i.e. if you call knit('path/to/input.Rnw'), the working dir will be temporarily switched to path/to/. If you want to know the input dir in code chunks, currently you can call an unexported function knitr:::input_dir() (I may export it in the future).
Starting from gsk3's Seb's suggestions, here's an idea:
the combination of username (login) and IP or name of the computer could be used to select the right directory.
That leads to something like:
setwd (switch (paste (Sys.info () [c ("user", "nodename")], collapse="."),
user.laptop = "~/Messungen",
user2.server = "~/Projekte/Projekt/",
))
So there is an automatic solution, that
works with source
works with Sweave
even works for interactive sessions where the commands are sent line by line
the combination of user and nodename of course needs to be specific
the paths need to be edited by hand, though.
Improvements welcome!
Update:
Gabor Grothendieck answered the following to a related question on r-help today:
this.dir <- dirname(parent.frame(2)$ofile)
setwd(this.dir)
which will work for source.
Another update: I now do most of the data analysis work in RStudio. RStudio's projects basically solve the problem: RStudio changes the working directory to the project root directory every time I switch between projects.
I can therefore put the project directory as far down my directory tree as I want (and the students can also put their copy wherever they want) and sync the data files and scripts/.Rnws via version control (We use a private git server). The RStudio project files are kept out of the version control, i.e. .gitignore contains .Rproj.user.
Obviously, within the project, the directory structure needs to be synchronized.
You can use sys.calls() to get the command used to source the file. Then you need a bit of trickery using regular expressions to get the pathname, bearing in mind that source("something/filename") could have used either the absolute or relative path. Here's a first attempt at putting all the pieces together: try inserting the following lines at the top of a source file.
whereFrom=sys.calls()[[1]]
# This should be an expression that looks something like
# source("pathname/myfilename.R")
whereFrom=as.character(whereFrom[2]) # get the pathname/filename
whereFrom=paste(getwd(),whereFrom,sep="/") # prefix it with the current working directory
pathnameIndex=gregexpr(".*/",whereFrom) # we want the string up to the final '/'
pathnameLength=attr(pathnameIndex[[1]],"match.length")
whereFrom=substr(whereFrom,1,pathnameLength-1)
print(whereFrom) # or "setwd(whereFrom)" to set the working directory
It's not very robust—for instance, it will fail on windows with source("pathname\\filename"), and I haven't tested what happens if you have one file sourcing another file—but you might be able to build a solution on top of this.
I have no direct solution how to obtain the directory of the file itself but if you have a limited range of directories and directory structures you can probably use
if(file.exists("c:/somedir")==TRUE){setwd("c:/somedir")}
You could check out the pattern of the directory in question and then set the dir. Does this help you?
An additional problem is that the working directory is a global variable, which can be changed by any script, so if your script calls another script, it will have to set the wd back. In RStudio I use Session -> Set Working Directory -> To Source File Location (I know, it's not ideal), and then my script does
wd = getwd ()
...
source ("mySubDir/myOtherScript.R", chdir=TRUE); setwd (wd)
...
source ("anotherSubDir/anotherScript.R", chdir=TRUE); setwd (wd)
In this way one can maintain a stack of working directories. I would love to see this implemented in the language itself.
This answer works for source and also inside nvim-R - I have no idea if it works with knitr and similar things. Any feedback appreciated.
If you have multiple scripts source-ing each other, it is important to get the correct one. That is, the largest i for which sys.frame(i)$ofile exists.
get.full.path.to.this.sourced.script = function() {
for(i in sys.nframe():1) { # Go through all the call frames,
# in *reverse* order.
x = sys.frame(i)$ofile
if(!is.null(x)) # if $ofile exists,
return(normalizePath(x)) # then return the full absolute path
}
}
This question is for those of you who happen to use R, on a Mac, in combination with Macromate's [Textmate](http://macromates.com/) text editor and the "R" Bundle. All of which are nifty, needless to say, but that's beside the point for now :-)
I've got a .RProfile file sitting in my default "~" startup directory, and it's got a number of useful functions in it I like to have access to when writing R scripts. But I also use Textmate for most of my writing, and the cmd-R functionality to to run my scripts within Textmate.
At the moment, I don't know how to tell Textmate where my .Rprofile is.
Is there a way--most likely through Textmate's Bundle settings--that I can point Textmate to my .RProfile so I don't have to write my functions into every script on a per-script basis?
OR
Is it actually better to include any custom functions in any script I write, so that anyone with a basic R setup can source and run my scripts?
I feel like I must be missing a dead-easy setting or config file here within either Textmate or the R environment it calls to run my scripts.
Thanks so much in advance!
The R Bundle Developer is apparently working on this (see this Post on the Mailing List) but it's not available at the moment.
In the meantime, you have a couple of choices.
First, you can create a new bundle (e..g, "briandk-R") then create a snippet w/in that bundle either with 'source($1)' or just hardcode the file you want to source instead of the placeholder (so, e.g., "source("~/some_file_to_source.R"). If you do the latter, then you can configure TM to source your file via a tab trigger (in the Bundle Editor, toggle over to 'settings' (upper left hand corner) and type "source.r, source.rd.console" in the 'Scope Selector' field then choose a few letters for your tab trigger (e.g., "src.")
If you don't want to do that, go to the 'Rdaemon' Directory (which is either in your home directory or in ~/Library/Application Support/Rdaemon). Look in this directory and you will see another directory called "daemon.' In there is a file called "start.r" which lists the files that are sourced upon starting R from the Rdaemon. You know what to do from there. (Note: This directory also contains a couple of other scripts which contain initial settings; you might wish to have a look at those as well)
The first part of Doug's response offers the simplest immediate solution... add
source('/Users/briandk/.Rprofile')
to the head of any .r files you want those functions in... with that one line of code, you get your utility functions. Of course, that only helps if you're running the whole TM file.
Ideally, the bundle will be updated... perhaps to support a shell variable via TM's preferences???
TM_RPROFILE
which could be set to the path to your .Rprofile file.
I just hacked this into tmR.rb with just 2 lines of code. To implement this, go to ~/Library/Application Support/TextMate/Pristine Copy/Bundles/ and Show the Contents of R.tmbundle
In there, you'll find support/tmR.rb
in my version, near line 112, you should change
tmpDir = File.join(ENV['TMP'] || "/tmp", "TM_R")
recursive_delete(tmpDir) if File.exists?(tmpDir) # remove the temp dir if it's already there
Dir::mkdir(tmpDir)
# Mechanism for dynamic reading
# stdin, stdout, stderr = popen3("R", "--vanilla", "--no-readline", "--slave", "--encoding=UTF-8")
stdin, stdout, stderr, pid = my_popen3("R --vanilla --slave --encoding=UTF-8 2>&1")
# init the R slave
stdin.puts(%{options(device="pdf")})
stdin.puts(%{options(repos="#{cran}")})
to
tmpDir = File.join(ENV['TMP'] || "/tmp", "TM_R")
recursive_delete(tmpDir) if File.exists?(tmpDir) # remove the temp dir if it's already there
Dir::mkdir(tmpDir)
rprofile = (ENV['TM_RPROFILE'] == nil) ? "" : "source('" + ENV['TM_RPROFILE'] + "')"
# Mechanism for dynamic reading
# stdin, stdout, stderr = popen3("R", "--vanilla", "--no-readline", "--slave", "--encoding=UTF-8")
stdin, stdout, stderr, pid = my_popen3("R --vanilla --slave --encoding=UTF-8 2>&1")
# init the R slave
stdin.puts("#{rprofile}")
stdin.puts(%{options(device="pdf")})
stdin.puts(%{options(repos="#{cran}")})
Just added 2 lines there... the one that begins "rprofile =" and the one that includes "#{rprofile}"
-Wil