[R] getOption() versus Sys.getenv

[Henrik Bengtsson]

There's also the alternative to use both, e.g. by having a system
environment variable set a corresponding R option, which then can be
overridden using options().  For instance, the R option mc.cores,
which is used by the parallel package, is set to the (integer) value
of system environment variable MC_CORES, iff set. Conceptually, when
the parallel package is loaded, the following takes place:

if (is.null(getOption("mc.cores")) {
  cores <- as.integer(Sys.getenv("MC_CORES"))
  if (!is.na(cores)) options(mc.cores = cores)
}

Example:

$ Rscript -e "library(parallel); getOption('mc.cores')"
NULL

$ MC_CORES=2 Rscript -e "library(parallel); getOption('mc.cores')"
[1] 2

$ MC_CORES=2 Rscript -e "options(mc.cores = 4); library(parallel);
getOption('mc.cores')"
[1] 4

/Henrik


On Fri, Aug 25, 2017 at 10:33 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> On 25/08/2017 1:19 PM, Sam Albers wrote:
>>
>> Hi there,
>>
>> I am trying to distinguish between getOption() and Sys.getenv(). My
>> understanding is that these are both used to set values for variables.
>> getOption is set something like this: option("var" = "A"). This can be
>> placed in an .Rprofile or at the top of script. They are called like this
>> getOption("var").
>>
>> Environmental variables are set in the .Renviron file like this: "var" =
>> "A" and called like this: Sys.getenv("var"). I've seen mention in the httr
>> package documentation that credentials for APIs should be stored in this
>> way.
>>
>> So my question is how does one decide which path is most appropriate? For
>> example I am working on a package that has to query a database in almost
>> every function call. I want to provide users an ability to skip having to
>> specify that path in every function call. So in this case should I
>> recommend users store the path as an option or as an environmental
>> variable? If I am storing credentials in an .Renviron file then maybe I
>> should store the path there as well?
>>
>> More generally the question is can anyone recommend some good
>> discussion/documentation on this topic?
>
>
>
> The environment is set outside of R; it's really part of the operating
> system that runs R.  So use Sys.getenv() if you want the user to be able to
> set something before starting R.  Use Sys.setenv() only if your R program is
> going to use system() (or related function) to run another process, and you
> want to communicate with it.
>
> The options live entirely within a given session.
>
> The .Renviron and .Rprofile files hide this difference, but they aren't the
> only ways to set these things, they're just convenient ways to set them at
> the start of a session.
>
> Duncan Murdoch
>
>
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