On 23/10/2020 9:25 p.m., Therneau, Terry M., Ph.D. via R-devel wrote:
I found an issue with the data() command this evening when working on the
survival package.
1. I have a lot of data sets in the package, almost all used in at least one
vignette,
help file, or test. As a space saving measure, I have bundled many of them
together,
i.e., the file data/cancer.rda contains 19 data sets, many of them small. The
resulting
file (using xz compression) is quite a bit smaller than the individual ones.
(I still get
a warning note about size from R CMD check, but I'm no longer 2x the limit.)
2. Consider the lung data set. All of these fail:
data(lung)
data("lung")
data(lung, package="survival")
a. The lung.Rd file had \usage{data(lung)}; that error was not caught by R
CMD check.
(Several other .Rd files as well.)
b. In broader examples for teaching, I sometimes load data from other
packages, e.g
data(aidssi, package="mstate"). But this does not work for survival. (The
larger
survival data sets that are in separate .rda files can be found.)
c. What does work is survival::lung. Might it be useful to add a comment to
data.Rd to
this effect?
You don't describe how this dataset is being included in your package.
Have you moved it from data/lung.rda to data/cancer.rda? Currently (in
survival 3.2-7) each of these works for me:
library(survival); data(lung)
library(survival); data("lung")
# Without library(survival):
data(lung, package="survival")
I think if the lung dataset is now being included in cancer.rda, you'd need
data(cancer, package="survival")
or equivalent to load it (and the rest of the datasets there).
3. Creating a separate package 'survivaldata' is of course one route, and is
suggested in
the "Writing R Extensions" guide. But this is not possible since survival is a
recommended package: it can't load any non-recommended package for it's tests or
vignettes. Longer term, perhaps there is way around this constraint?
Maybe the solution is to put your datasets into the "datasets" package,
or make "survivaldata" a recommended package, or just leave things as
they are and ignore the warnings about package size. I think that's a
negotiation you should have with R Core.
Duncan Murdoch
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