[BioC] adding environment variables

[Martin Morgan]

On 10/28/2010 07:40 AM, Sean Davis wrote:
> On Thu, Oct 28, 2010 at 10:21 AM, Robert M. Flight <rflight79 at gmail.com>wrote:
> 
>> Hi All,
>>
>> I am developing a package that requires information about the location
>> of a set of files that will be used often in the calculations. In my
>> current version, I define the location in the main file that calls all
>> the subfunctions. This works fine when you are installing from source,
>> but will not work so well if I want people to be able to install
>> binary versions of the package. Therefore, I think the best way to
>> encode the information would be through the use of an environment
>> variable, that could then be read by "Sys.getenv(VARIABLE)" when the
>> function is called.
>>
>> In the help, I found a few different ways to set environment
>> variables, but the easiest way (from my reading anyways) seemed to be
>> by creating the file "Renviron.site" in the R_HOME/etc directory and
>> adding the variable there. I am interested in opinions from the list,
>> or other suggestions on how to do this.
>>
>> For those who are interested, the package does a lot of parsing of
>> KEGG KGML files, and to speed up calculations I offer advice that they
>> should download a copy of the KGML directory for their organism to
>> their local machine, and I want the package to know where those files
>> are at runtime.
>>
>>
> You could also use an option or set of options.  See ?options for details.

Or define an environment to store relevant information and accessors for
you / the user to set / get

.kgmlOptions <- new.env(parent=emptyenv())

setKgmlLocalRepository <-
    function(x) .kgmlOptions[["localRepository"]] <- normalizePath(x)

getKgmlLocalRepository <-
    function() .kgmlOptions[["localRepository"]]

If there's just the single option then active bindings could be fun, in
a package implemented I think as

.onLoad <-
    function(...)
{
    makeActiveBinding("kgmlLocalRepository", function(x) {
        if (missing(x)) .kgmlOptions[["localRepository"]]
        else .kgmlOptions[["localRepository"]] <- normalizePath(x)
    }, topenv(parent.frame()))
}

and used as any variable, both in and outside the package.

kgmlLocalRepository <- "some-dir"
kgmlLocalRepository

This latter is probably too clever -- the user isn't aware enough that
they're setting a package-global variable.

Martin

> 
> Sean
> 
> 
>> Thanks in advance,
>>
>> -Robert
>>
>> Robert M. Flight, Ph.D.
>> University of Louisville Bioinformatics Laboratory
>> University of Louisville
>> Louisville, KY
>>
>> PH 502-852-0467
>> EM robert.flight at louisville.edu
>> EM rflight79 at gmail.com
>>
>> Williams and Holland's Law:
>>        If enough data is collected, anything may be proven by
>> statistical methods.
>>
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>>
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