On Thu, 12 Nov 2009, Robin Hankin wrote:
Hi
[R-2.10.0; suse linux]
I am having difficulty creating S4 objects in the data directory of a
package. I want
to create a bunch of simple S4 objects for use in the examples section of the
Rd files.
It says in R-exts that:
" R code should be “self-sufficient” and not make use of extra functionality
provided by the package, so that the data file can also be used without
having to load the package"
My current minimal self-contained example follows.
le112:~% cat ./anRpackage/R/f.R
setClass("foo", representation=representation(x="numeric"))
le112:~% cat ./anRpackage/data/toy_foo.R
"toy_foo" <- new("foo",x=rep(2,7))
fails R CMD check (transcript below)
It fails because the class isn't defined. I can
add 'require(anRpackage)' to the toy_foo.R
but I'm not sure if this is consistent with the above
advice in R-exts (and it
fails R CMD check anyway).
It isn't consistent.
What is best practice for creating a package with
"toy" S4 objects for use in the examples section
of the Rd files?
Why not do this either in the examples section, or in a
make_data_for_examples() function in the package?
I see the data() mechanism as having been largely superseded by
lazy-loading. It was primarily a way to avoid having large datasets
always loaded (and taking up memory and gc() time). It is sometimes
convenient to load a dataset from a package without loading that
package: see the help for 'alias' and 'logLik' for example, but if you
don't need that possibility (and it seems that in your case it is not
available to you) you might as well have the object lazy-loaded in the
package or accessed by an accessor function in the package.
cheers
Robin
le112:~% R CMD check ./anRpackage
* checking for working pdflatex ... OK
[snip]
* checking data for non-ASCII characters ... NOTE
Error: "foo" is not a defined class
Call sequence:
8: stop(gettextf("\"%s\" is not a defined class", Class), domain = NA)
7: getClass(Class, where = topenv(parent.frame()))
6: new("foo", x = rep(2, 7))
5: eval(expr, envir, enclos)
4: eval(i, envir)
3: sys.source(zfile, chdir = TRUE, envir = envir)
2: switch(ext, R = , r = {
library("utils")
sys.source(zfile, chdir = TRUE, envir = envir)
}, RData = , rdata = , rda = load(zfile, envir = envir), TXT = ,
txt = , tab = , tab.gz = , tab.bz2 = , tab.xz = , txt.gz = ,
txt.bz2 = , txt.xz = assign(name, read.table(zfile, header = TRUE,
as.is = FALSE), envir = envir), CSV = , csv = , csv.gz = ,
csv.bz2 = , csv.xz = assign(name, read.table(zfile, header = TRUE,
sep = ";", as.is = FALSE), envir = envir), found <- FALSE)
1: utils::data(list = f, package = character(0L), envir = dataEnv)
Execution halted
Portable packages use only ASCII characters in their datasets.
* checking examples ...no parsed files found
NONE
WARNING: There were 2 warnings, see
/home/rksh/anRpackage.Rcheck/00check.log
for details
le112:~%
--
Robin K. S. Hankin
Uncertainty Analyst
University of Cambridge
19 Silver Street
Cambridge CB3 9EP
01223-764877
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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