How to Make R Read My Environmental Variables

How can I make R read my environmental variables?

You want Sys.getenv() as in Sys.getenv("PATH"), say.

Or for your example, try

SIR <- Sys.getenv("SIR")   
system(paste("ec2-cancel-spot-instance-requests",  SIR))

As for setting variables at startup, see help(Startup) to learn about ~/.Renvironment etc

Accessing environment variables set in R session from shell

The environmental variable dies with the process.

Each process has its own set of environmental variables, inherited from the parent process. When you create the environmental variable BLAH, you create it in the environment of the R process you're running, but not in the environment of the parent process.

If you want another process to access this environmental variable, you'll need to start the process from within R. Then the child process will inherit BLAH. This documentation for Sys.setenv mentions this:

Sys.setenv sets environment variables (for other processes called from within R or future calls to Sys.getenv from this R process).

For example:

Sys.setenv(BLAH="blah")
system("echo $BLAH")
# blah

How to access a bash environment variable from within R in emacs-ess

I don't know about R and self-defined environment variables, but I set the PATH variable in emacs to the same value as in my bashrc. I modified my code to your problem, give it a shot and let me know if it works.

;; set env variable in Emacs
(getenv "SETTINGS")
(setenv "SETTINGS" "/home/user/settings.xml")

Original code (for PATH) is:

;; Emacs has its own path variable
(getenv "PATH")
 (setenv "PATH"
(concat
 "/usr/local/texlive/2011/bin/x86_64-linux" ":"
(getenv "PATH")))

Reading global environment from within a function in R

Probably cleanest to pass the environment:

fun <- function(envir = parent.frame()) ls(envir = envir)
fun()

This lists the objects in the caller but also lets the user change which environment is used. For example, they could force the global environment to be used:

fun(.GlobalEnv)

set environment variables for system() in R?

I think you are confusing the issue. I fear this may be about login shells versus non-login shells. See the bash manual page for the fine print ... which has driven me bonkers in the past.

That said, if you can set environment variables system-wide, you have a few options:

/etc/environment is a very good place as it is shell-agnostic should you ever use a different shell
for login versus non-login shells, the one way to get complete control that I found suitable was to put my changes into something like ~/.local_bashrc
the add . ~/.local_bashrc from and and all of
- ~./bashrc
- ~/.bash_profile
- ~/.profile`
etc pp.

You can precede the sourcing with a echo Hello from FILE where you replace FILE with the name of the file. That shows you the difference between shells starting from login (eg via gdm et al), via ssh connection, via new xterm etc terminals and so on.

Accessing R's Environmental Variables from Bash

It may be easier than the two earlier answers suggest:

Because RHOME is so central, do R RHOME:

edd@don:~$ R RHOME
/usr/lib/R
edd@don:~$ val=$(R RHOME)
edd@don:~$ echo ${val}
/usr/lib/R
edd@don:~$

Essentially all others are available via R CMD config ...

edd@don:~$ R CMD config --help | head -20
Usage: R CMD config [options] [VAR]

Get the value of a basic R configure variable VAR which must be among
those listed in the 'Variables' section below, or the header and
library flags necessary for linking against R.

Options:
  -h, --help            print short help message and exit
  -v, --version         print version info and exit
      --cppflags        print pre-processor flags required to compile
            a C/C++ file using R as a library
      --ldflags         print linker flags needed for linking a front-end
                        against the R library
      --no-user-files  ignore customization files under ~/.R
      --no-site-files  ignore site customization files under R_HOME/etc

Variables:
  BLAS_LIBS     flags needed for linking against external BLAS libraries
  CC            C compiler command
  CFLAGS        C compiler flags
edd@don:~$

Lastly, for a running R session you can start one and access it:

edd@don:~$ Rscript -e 'cat(Sys.getenv("PATH"))'     # manual break
/home/edd/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:\
/sbin:/bin:/usr/games:/usr/local/gamesedd@don:~$