R devel - Oct 2003 - Accessing data files w/ --use-zip-data

I have encountered an issue while preparing some of the Bioconductor
packages for our upcoming release, and Duncan Murdoch suggested that I
bring one of the related points up here.

The background is that we are building our packages under Windows with
"Rcmd install --build" which will flag the zip options.  When the
total
size of files in <pkg>\data are over a certain threshold of size (100k
IIRC) the will be zipped in a file named Rdata.zip to save space.  So far,
so good.

The problem arose in that at least one of the packages in the BioC suite
is directly acccessing files in the data directory and not going through
the data() command or related functions - and in this case the package
authors are doing it in .First.lib() which causes the package loading to
fail.

The issue that Duncan suggested I raise is whether or not it should be
considered accepted behaviour for a package author to be accessing files
in <pkg>\data (at this time I don't know the reasoning behind the
specific
example here, I just know that that's what they've done) or if this
should
be considered a Bad Thing.

Thanks
-Jeff

Jeff Gentry wrote:
>...
>The issue that Duncan suggested I raise is whether or not it should be
>considered accepted behaviour for a package author to be accessing files
>in <pkg>\data (at this time I don't know the reasoning behind the
specific
>example here, I just know that that's what they've done) or if this
should
>be considered a Bad Thing.
>
I do this in some instances where I have data in a format not supported 
by data(), for example,  database files that are used by package 
programs or tests (but I have always wondered if it is "the right"
thing
to do).  If it is considered a Bad Thing then there needs to be another 
location for files like this, perhaps inst/data or something like that.

Paul Gilbert

Hi all,
> The issue that Duncan suggested I raise is whether or not it should be
> considered accepted behaviour for a package author to be accessing files
> in <pkg>\data (at this time I don't know the reasoning behind the
specific
> example here, I just know that that's what they've done) or if this
should
> be considered a Bad Thing.
Examples are the makecdfenv und matchprobes packages, part of which I
wrote. They deal with data formats that are external to R, namely vendor
(Affymetrix) specific file formats, and provide tools for importing these
data into R. For the examples / vignettes, I need to provide example data
files. Up to now I am putting them into the data directory, and access
them with

specializedImportFunction(file.path(.path.package("matchprobes"),
                          "data", "HG-U95Av2_probe_tab.gz"),
...)

Is this considered offensive to the R package structure? Whereelse to put
data that comes in specialized (not .rda, .txt, .csv) formats?

Thanks
  Wolfgang