[BioC] adding environment variables

[Robert M. Flight]

Wow, I see what you are doing there, and it looks like it would be a
good way to do it. I may investigate that in the future.

In the interest of staying simple and what I can figure out right now
that would work, I actually went with the suggestion of using an
object to store the information. This object is created by a very
simple function, and is stored in the directory of the package. It is
easy to modify the object, and only has to be done once after
installation, if it is even used.

Thanks for the suggestions.

-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.



On Thu, Oct 28, 2010 at 12:49, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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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>>
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>
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