[BioC] adding environment variables

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Oct 28 16:43:14 CEST 2010

I would use some object to encode the file location.  The object might
have additional information as well.  Conceptually, this is similar to
how biomaRt has a mart object which specifies a biomart server.

You can do the same with options or environment variables, however,
for your use case I would find it unnatural.  Specifically because
your files are data as opposed to executables/libraries.


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.
> 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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