When I start my R session (under windows 7), I get this error message:
Error: '\U' used without hex digits in character string starting ""C:\U"
I know what the problem is here: Somewhere, there is a directory being set to c:\USERS\something where the \ needs to be a \\ or a /. However, I do not know where it is.
My R_HOME/etc directory has an Rprofile.site file, but no .Rprofile and no .Renviron file.
My HOME directory has neither file.
My HOME/R/win-library/R_Library/base/R directory has an Rprofile file (no period) but no .Rprofile, and no .Renviron
My working directory has neither file.
The R_ARCH directory contains nothing R-related.
I identified all these directories with Sys.getenv().) Of the directories shown there, about 30 display as formed with (single) \'s, while nine are displayed as formed with (single) /'s. There is more than one C: Users directory with the slash going each way.
A computer-wide file search found no instances of either .Rprofile or .Renviron.
So where is this setting? And why does my R installation work at all, with 3/4 of the paths defined in environment variables going one way, and 1/4 of the paths (but still a lot of paths) going the other?
I'll bet it doesn't happen if you start it from cmd.exe with r --vanilla. Find all .Rdta or .Rdata files and rename them to bak version. Same for the .Rhistory files. May need to look inside the .rprofile.site file and see if it has been taken over by some gremlin. In Windows (and Macs), the "dot-files are usually hidden and you use magical incantations to expose them. The number of directories with solitary backslashes displayed in returns from Sys.getenv() should be zero.
Related
When creating filepaths and URLs, I noticed that many times the path starts with ./ or ~/.
What is the difference between filepaths that start with ./ and ~/?
What do each of them mean?
For the sake of completeness ...
Just path is a file or directory named path in the current directory.
./path is a file or directory named path in the current directory, with the directory spelled out. The dot directory . represents the current directory, and path is the name of the file or directory within this directory.
~/path is a shorthand for $HOME/path where $HOME is a variable which refers to your home directory. Typically your home directory will be somewhere like /home/you or /Users/you where you is your account name. (The command echo "$HOME" will display your home directory.) The expanded value is an absolute path (unless you have messed up the value of $HOME thoroughly), as indicated by the initial slash.
/path is an absolute path which refers to a file or directory named path which is in the root directory /. Every file on Unix is ultimately somewhere in the directory tree which starts with the root directory.
A file name which begins with $ includes the value of a shell variable in its name (like for example $HOME above); you have to know the value of that variable to determine whether it ends up containing a relative or an absolute path. Similarly, ~ at the beginning of a file name gets replaced ("expanded") by the shell to a different string, as outlined above.
(Technically, it's possible for a file name to begin with a literal dollar sign or tilde, too; you would then have to quote or backslash-escape that character to avoid having the shell expand it to something else. This is rather inconvenient, so these file names tend to be rare in practice.)
In the following exposition, we refer to the result of any such replacements, and ignore the complication of possible quoting.
Every file name which begins with / is an absolute path (aka full path) which explains how to reach a particular node starting from the root directory. For example, /var/tmp/you/reminder.txt refers to a file or directory reminder.txt (probably a file, judging from the name; but Unix doesn't care what you call your files or directories) which is in the directory you which is in the directory tmp which is in the directory var which is in the root directory.
Every file name which doesn't begin with / is a relative path which indicates how to reach a particular file or directory starting from the current directory. The special directory .. is the parent directory (that is, the directory which contains this directory) and the special directory . is the current directory. So path/there refers to the file or directory there inside the directory path in the current directory; and (hover the mouse over the gray area to display the spoiler)
there/.././and/back/.. is a (wicked complicated) way to refer to the directory and in the current directory, where we traverse the there directory and then move back to the current directory; then stay in the current directory; then refer to the directory back inside the directory and, but then move back to the parent directory of that, ending up with ./and.
In addition to ~/ for the current user's home directory, some shells and applications allow the notation ~them/ to refer to the home directory of the user account them. Also, some web server configurations allow each user to have a public web site in their directory ~/public_html and the URL notation http://server/~them/ would serve up the site of the user account them for outside visitors.
The current directory is a convenience which the shell provides so you don't have to type long paths all the time. You can, if you want to.
/bin/ls /home/you/Documents/unix-101/directories.txt
is a longwinded but perfectly valid way to say (assuming you are in your home directory),
ls Documents/unix-101/directories.txt
You could also say
cd Documents/unix-101
ls directories.txt
and until you cd again, all your commands will run in this directory.
See What exactly is current working directory? for a longer exposition of this related concept.
A "directory" is sometimes called a "folder" by people who are not yet old enough to prefer the former.
Tangentially, don't confuse the directory name . with the Bourne shell command which comprises a single dot (also known by its Bash alias source). The command
. ./scriptname
runs the commands from the file ./scriptname in the context of the current shell instance, as opposed to in a separate subshell (which is what just ./scriptname does). In other words, this command line invokes the dot command on a file scriptname in the dot directory.
The Bourne shell (and derivatives like Bash, Zsh, etc) use single quotes to prevent variable expansion and wildcard expansion, and double quotes to permit variable expansion, but inhibit wildcard expansion in a string. The quoting rules on Windows are different, and generally use double quotes to keep whitespace-separated values as a single string (and % instead of $ for variable substitutions).
./ means "starting from the current directory". . refers to the current working directory, so something like ./foo.bar would be looking for a file called foo.bar in the current directory. (As a side note, .. means refers to the parent directory of the current directory. So ../foo.bar would be looking for that file one directory above.)
~/ means "starting from the home directory". This could have different meanings in different scenarios. For example, in a Unix environment ~/foo.bar would be looking for a file called foo.bar in your home directory, something like /home/totzam/foo.bar. In many web applications, ~/foo.bar would be looking for a file called foo.bar in the web application root, something like /var/http/mywebapp/foo.bar.
./ is the current directory
~/ is the home directory of the current user
./ means that path is relative to your current position.
~/ means that path is relative to your home directory.
I will explain a simple example of it. As developers mentioned:
./ is current directory.
~/ is the home directory of the current user.
How both of the file path expressions can help us? Suppose you want to execute a script (.sh) and you're in the same directory where file exists then you can simply do it ./filename.sh
I mostly use ~/ to access my home directory files like .bashrc when I want to add any config in it. It's easier since the file path expression (for home directory) feels much easier and makes accessibility to the file from anywhere, without worrying about the path or changing the path.
. represents current directory
.. represents the parent directory
~ represents the home directory for the current user. Home directory is also represented by HOME env variable. you can do echo $HOME on the shell to see it.
These are generally used to specify relative paths. The / in the end of each notation is a separator that you can use when using these notations together.
Ex:
$ cd ../.. # Go 2 directories backwards
$ cd ~ # Takes you to $HOME directory
$ cd . # Does nothing :) As it literally means go to the directory that you are already present in.
$ cd ~/dir1 $ go to `$HOME/dir1`
On Unix, in any directory if you do ls -a you would see that . and .. will be mentioned (even for empty directory). Like mentioned, these have special meaning and are generated by default in Unix systems and are generally helpful to specify relative paths (i.e, path to a different directory relative to your current directory)
cd command is harmless. So, just play around by combining notations with cd command. You will eventually get a grip of them.
I have a "copy deployed" installation of R with no R-specific environment variables set.
I want to source a file from within Rprofile.site:
source("how/to/find/this/file/my_settings.R")
Where could I place my my_settings.R file so that it can be found from within Rprofile.site no matter in which path Rprofile.site is installed?
BTW: I want to avoid an absolute path to my_settings.R this would work indeed. I'd prefer to use the same folder as Rprofile.site or a path relative to it to support copy deployment of R.
Edit 1: The problem is that getwd is always different depending on the current folder from which you start R
If you can't use absolute paths and that your working directory is not stable, one way is to use .libPaths or .Library.
By default your Rprofile should be in directory paste0(.Library,"/../etc/") or paste0(.libPaths()[2],"/etc/") so you can put your file there and source it with :
source(paste0(.Library,"/../etc/my_settings.R"))
source(paste0(.libPaths()[2],"/etc/my_settings.R"))
As far as I understand the first option is stable (I don't think one can change the value of .Library).
If you use the second option just make sure that if in the future you alter your .libPaths() you do it after sourcing your file.
See ?.libPaths for more info on default folders.
I constantly need to call Tex Live binaries for compilation in R. However after the upgrade of Tex Live distribution, the path to current binaries needed to updated manually in the PATH(Sys.getenv("PATH")) variable.
As a single user on a Ubuntu system, which file should I update the value in, so that R gets the PATH correctly irrespective of whichever directory R is launched from.
One point I still don't gather is from where does R gets its site-wide (I mean for all users, even if faulty in saying so) PATH variable set, because no such variable name as "PATH" occur inside any files (Renviron, Renviron.site, Rprofile.site) in either of "R_HOME/etc/" and user's home directory? I also haven't set Sys.getenv("R_ENVIRON") and Sys.getenv("R_ENVIRON_USER") values.
I'd appreciate anybody's input here.
#JeffreyGoldberg's solution was close, but not quite right.
Rprofile files are interpreted as R code
Renviron files can only contain name value pairs, and are not interpreted as R code
From the help for Startup:
Note that there are two sorts of files used in startup: environment files which contain lists of environment variables to be set, and profile files which contain R code.
I'm not sure if this question is asking specifically how one can set the site wide value of PATH, rather than PATH for one specific user, but there are three locations you can put these files.
A project directory (i.e., a directory you choose to launch R from)
HOME
R_HOME/etc
These locations are searched in the order numbered above. The first location can contain configurations specific to a project, the second contains those specific to a user, and the third, site wide configuration settings. When a file is found it is used, so local takes precedence over global. Don't think you can create a more specific version that simply updates what you've done in a more general configuration file. R_HOME/etc/Renviron is created on installation and should not be edited. You may create a file called R_HOME/etc/Renviron.site, but do not edit R_HOME/etc/Renviron.
To create a site wide value of PATH, you will want to set it in a file in R_HOME/etc. Here you can use either Renviron.site or Rprofile.site for the file name. For a file in R_HOME/etc, Do not use Renviron, Rprofile, .Renviron, or .Rprofile for the name of a profile or environment file in this location. You can find out what R_HOME is in an R session using R.home(), or Sys.getenv("R_HOME")
To create a PATH value for a single user, set it in a file in HOME, which you can find in your R session using Sys.getenv("HOME") or path.expand("~"). You can also just use "~" to refer to HOME. Here, an Renviron file should be ~/.Renvironand an Rprofile file ~/.Rprofile. Take note of the difference between how profile and environment files are named in your HOME directory vs. R_HOME/etc
To create a PATH for a single project, set it in a file in that project's top level directory. Name the files as you would in your home directory (.Rprofile or .Renviron).
If you are creating an Renviron file, the file should include the following line:
PATH=<your path>
< and > should not be included. An example would be:
PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
If you are creating an Rprofile file, the file should include the following line:
Sys.setenv("<your path>")
again, don't include "<" or ">". An example would be:
Sys.setenv("/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin")
There are various ways of doing this that get and edit a PATH variable (e.g., tack on a new path at the end, or the beginning). You can also use the strategy of setting an environment variable if it doesn't already exist and/or doesn't contain something you want it to. I've come to prefer just setting up my path simply, and coding it directly.
One final note, if you run R from a command line interface, environment variables may be inherited from your shell. RStudio also has its own startup sequence and may modify the end of your PATH variable. It should start as it is defined in your Rprofile or Renviron files. The R Console app itself has the fewest quirks with system environment variables, and should accept your path exactly as it is set with an Rprofile or Renviron file.
Edit: I should have tested before posting. What I describe below did not work. (Down voting my own answer is a strange thing.)
On my system (macOS, bash), R.app is not picking up my $PATH from my shell environment or .profile. However RStudio is picking it up. I do not understand the different behaviors.
One way to get consistent behavior would be to specify this in an Renviron file.
If you create a file named .Renviron in your come directory with a line like
Sys.setenv(PATH="/opt/local/bin:usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Library/TeX/texbin")
(but of course with the path elements you need) that should give you consistent behavior.
The downside is that you need to manually maintain this. I suppose you could run a script from one of your other start up scripts that generated the .Renviron file. But either way, I consider this whole thing a work around in place of actually understanding where R picks up its environment from.
I would like to know how I can set the pdflatex path in R to use sweave. Because I have 2 different MikTeX installations and one is working properly. Please take into account that I am using R (RStudio) in Windows. I found some suggestion however, for Linux or Unix users.
thanks in advance
If you have multiple installs of LaTeX (i.e. MikTeX) and you want to use a specific one of these, then you need to make sure that R finds the one you need first. This means that you have to add the location of your preferred version of pdfLaTeX at the front of your PATH system environment variable.
If you do not have administrator rights in Windows, then you can use R's environment file to change the PATH variable for R only. See ?Startup in R for details on this process. Follow the following steps:
in R, check the output of Sys.getenv("R_ENVIRON"). This will return the full path to an existing environment file, but will be empty in most cases. If a file exists, skip to step 3 below.
if no path is returned in step 1, create a file Renviron.site in the folder R_HOME/etc where R_HOME is the path returned by Sys.getenv("R_HOME").
add a line to the environment file as follows: PATH=C:\\full\\path\\to\\the\\folder\\with\\pdflatex;"${PATH}" (the quotations marks are important)
restart R and check Sys.getenv("PATH") and Sys.which("pdflatex") returns the correct paths.
If you do not have rights to create a Renviron.site file in R_HOME\etc, then you can also create a .Renviron file in HOME (Sys.getenv("HOME")).
I am working with a "factory fresh" version of RStudio on Windows 7. R is installed under C:/Program Files which means the default libraries are stored here, and the two locations contained in .libPaths() on startup are both within this folder.
I want to work with another R library (igraph). Since the C:\Program Files folder is write-protected, I have set up another area to work in: C:\Users\nick\R and installed the igraph library in C:\Users\nick\R\library. I can manually add this location to the .libPaths() variable and use the library with no problems.
However, my problem is getting RStudio to automatically add this location to the .libPaths() variable on startup. I read that I could add the relevant command to my .Rprofile file - but I couldn't find any such file (presumably they are not automatically created when RStudio is installed). I then created a file called .Rprofile containing only this command. This only seemed to work when the .Rprofile file was saved in C:\Users\nick\Documents (which is the path stored in both the R_USER and HOME environmental variables). What I would like is to have the .Rprofile file stored in C:\Users\nick\R.
I have read all the information in ?Startup and it talks about where to store commands that run on startup. But I just can't make this work. For example there seems to be no way to change the location of the home directory without reading a file stored in the home directory. I don't seem to have any .Renviron files and creating these myself doesn't seem to work either.
I would really appreciate an answer in simple terms that explains how I could go about changing where the .Rprofile file is read from.
In Windows, you set the R_USER profile by opening up a command line and running:
SETX R_PROFILE_USER "C:/.../.Rprofile"
Where (obviously) the path is the path to your desired .Rpofile. In R, you can check that it worked:
Sys.getenv("R_PROFILE_USER")
Should return the path you specified. Note that you likely need to have all R sessions closed before setting the R_USER variable.