On Fri, 16 Apr 2010, Therneau, Terry M., Ph.D. wrote:
'Henrik' wrote:
I think what people are also thinking about is that the policy for
publishing a package on CRAN is that it have to pass R CMD check with
no errors, warnings *or* notes. So, in that sense notes are no
different from warnings.
I think that policy is a figment of his imagination. 'NOTE' was
introduced to allow tentative warnings: we for example note .Rd errors
that we can correct and warn (so far) on those we cannot.
---------------------------------
Getting rid of these notes would be very hard in the survival package.
The population survival routines (survexp, pyears) that have to deal
with dates try to be very accommodating wrt the date format the user
chose, so have constructions like
if (user date looks like a chron object) {
calculation using chron functions
}
else if (is from the date package) {
use mdy.date }
else if (Date object)
etc
Most of the functions inside the {} cause a warning note because of
course the necessary packages for each case are not present when
survival is built. Since we deal with medical studies that span
multiple years or even decades, I and others in my group benefit
directly from this date handling: it was not added solely from a
humanitarian impulse.
It's a minor nuisance, since I have to read through the messages after
each build to see if something I actually do need to worry about turns
up. It has happened, in which case I'm thankful for the message.
(Although it would be nice if there were a way to generate more context.
Once one was for an undefined variable 'n', which was not easy to find
using a text editor.)
We do load all the Depends and Suggests packages when doing the
codetools checks, so I think that
Suggests: date, chron, timeDate
would solve this. It leaves
predict.coxph: no visible global function definition for ‘labels.lm’
predict.coxph: no visible global function definition for ‘Build.terms’
predict.survreg: no visible global function definition for ‘labels.lm’
predict.survreg: no visible global function definition for ‘Build.terms’
survpenal.fit: no visible global function definition for ‘new.frame’
survpenal.fit: possible error in get("coxlist1", frame = rho): unused
argument(s) (frame = rho)
survpenal.fit: possible error in get("coxlist2", frame = rho): unused
argument(s) (frame = rho)
survreg.fit: no visible global function definition for ‘new.frame’
which are I think all from S-Plus specific code.
Brian Ripley
Terry Therneau
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Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
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