[R-pkg-devel] appropriate directory for data downloads in examples, demos and vignettes

[Jonathan Callahan]

Henrik,

Thanks for the detailed response! I'll have to look at the R.cache package
and try out your suggestions.

Jon

On Mon, Jun 29, 2015 at 12:48 PM, Henrik Bengtsson <
henrik.bengtsson at ucsf.edu> wrote:

> FYI,
>
> my R.cache package keeps cache files under a specific cache directory.
> To meet the CRAN Policies
> [http://cran.r-project.org/web/packages/policies.html] that:
>
> "Packages should not write in the users’ home filespace, nor anywhere
> else on the file system apart from the R session’s temporary directory
> (or during installation in the location pointed to by TMPDIR: and such
> usage should be cleaned up). Installing into the system’s R
> installation (e.g., scripts to its bin directory) is not allowed.
>
> Limited exceptions may be allowed in interactive sessions if the
> package obtains confirmation from the user."
>
> The R.cache root directory is setup as follows:
>
> 1. It can be specified via environment variable R_CACHE_PATH.  If that
> is not given, it defaults to ~/.Rcache/, i.e. effectively: rootpath <-
> Sys.getenv("R_CACHE_PATH", default="~/.Rcache").
>
> 2. Next, if and only if this directory exists, then no "questions
> asked" and this directory will be used as is.
>
> 3. If it does not exist and R runs in an interactive session, then the
> user is prompted whether s/he wish to create the directory given by
> the 'rootpath' rule above, e.g.
>
> > library(R.cache)
> The R.cache package needs to create a directory that will hold cache
> files. It is convenient to use one in the user's home directory,
> because it remains also after restarting R. Do you wish to create the
> '~/.Rcache/' directory? If not, a temporary directory
> (C:\Users\hb\AppData\Local\Temp\Rtmp0udmsF/.Rcache) that is specific
> to this R session will be used. [Y/n]:
>
> If user accepts, then the directory is created and we're back to Step
> 2 above (which will be the case for all future R sessions).
>
> 4. If the user don't want to create this directory, or R runs in a
> non-interactive session (e.g. R CMD check), then a temporary cache
> directory is used, which is rootpath <- file.path(tempdir(),
> ".Rcache").  This directory is only guaranteed to exist for the
> current session.
>
> Comment on ~/.Rcache/: This default was chosen because it can be
> created on all platforms and for all users.  I don't know of any other
> path (except one under tempdir()) for which this is true.  The
> downside is that it adds to the user's quota, will most likely be
> backed up by default etc. However, it is very easy to use file links
> to point it elsewhere, e.g. ln -s /vartmp/$USER/.Rcache ~/.Rcache/.
>
>
> If your GIS data is supposed to live beyond a single R session, then
> you could use a similar approach for your MazamaSpatialUtils package.
> You could emulate the above completely, e.g. MAZAMA_SPATIAL_PATH and
> ~/.mazama_spatial/.  Alternatively, you could leverage the R.cache
> package and simply put all your data in a subdirectory under the
> R.cache root path, e.g. getCachePath(dirs="MazamaSpatialUtils").  For
> most users this will become ~/.Rcache/MazamaSpatialUtils/.  With this,
> all required interactions with the user is taken care of by R.cache
> (as above) and it will also fallback to using a temporary directory
> when run under 'R CMD check'.k
>
>
> Either way, you definitely want to use tempdir() for a
> session-specific temporary directory, e.g.
>
> > tempdir()
> [1] "C:\\Users\\hb\\AppData\\Local\\Temp\\Rtmp0udmsF"
>
> It works on all platforms and you don't have to create your on "hash"
> subdirectory.
>
>
> /Henrik
> (author of R.cache)
>
> On Mon, Jun 29, 2015 at 9:22 AM, Paul Gilbert <pgilbert902 at gmail.com>
> wrote:
> > Regarding alternative places for scripts, you can add a directory (eg
> > inst/testLocalScripts) and then with a recently added R CMD feature you
> can
> > do
> >
> >  R CMD check --test-dir=inst/testLocalScripts your-package.tar.gz
> >
> > This will not (automatically) be checked on CRAN. Beware that you also
> need
> > to run R CMD check without this option to run your regular tests.
> >
> > Paul
> >
> >
> >
> > On 06/29/2015 11:25 AM, Jonathan Callahan wrote:
> >>
> >> Hi,
> >>
> >> The MazamaSpatialUtils
> >> <http://cran.r-project.org/package=MazamaSpatialUtils> package has a
> >> required "package state" variable which users set to specify where they
> >> want to store large amounts of GIS data that is being downloaded and
> >> converted by the package. The implementation of this follows Hadley's
> >> advice here:
> >>
> >> http://adv-r.had.co.nz/Environments.html#explicit-envs
> >>
> >> The functionality is implemented with package environment and getter and
> >> setter functions:
> >>
> >> spatialEnv <- new.env(parent = emptyenv())
> >> spatialEnv$dataDir <- NULL
> >>
> >>
> >> getSpatialDataDir <- function() {
> >>    if (is.null(spatialEnv$dataDir)) {
> >>      stop('No data directory found. Please set a data directory with
> >> setSpatialDataDir("YOUR_DATA_DIR").',call.=FALSE)
> >>    } else {
> >>      return(spatialEnv$dataDir)
> >>    }
> >> }
> >>
> >>
> >> setSpatialDataDir <- function(dataDir) {
> >>    old <- spatialEnv$dataDir
> >>    dataDir <- path.expand(dataDir)
> >>    tryCatch({
> >>      if (!file.exists(dataDir)) dir.create(dataDir)
> >>      spatialEnv$dataDir <- dataDir
> >>    }, warning = function(warn) {
> >>      warning("Invalid path name.")
> >>    }, error   = function(err) {
> >>      stop(paste0("Error in setSpatialDataDir(",dataDir,")."))
> >>    })
> >>    return(invisible(old))
> >> }
> >>
> >>
> >> My question is:
> >>
> >> *What is an appropriate directory to specify for vignettes (or demos or
> >> examples) that need to go through CRAN testing?*
> >>
> >> The R code in vignettes need to specify a directory that is writable
> >> during
> >> the package build process but that will also be available to users.
> >>
> >> Should we create a /tmp/<hash> directory? Would that be available on all
> >> systems?
> >>
> >> Alternatively,
> >>
> >> *What is an alternative to vignettes and demos for tutorial scripts that
> >> should not be tested upon submission to CRAN?*
> >>
> >>
> >> Thanks for any suggestions.
> >>
> >> Jon
> >>
> >>
> >
> > ______________________________________________
> > R-package-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>


-- 
Jonathan Callahan, PhD
Mazama Science
206-708-5028
mazamascience.com

	[[alternative HTML version deleted]]