Hi
I have submitted a package (rioja) to CRAN. It checks OK for all R versions
and OS's except r-release-macosx-ix86 where it fails when checking the
examples. Specifically, it fails because R can't find the package vegan which
is needed in a function. Here is the snippet from the check results:
### Begin snippet
checking examples ... ERROR
Running examples in 'rioja-Ex.R' failed.
The error most likely occurred in:
> ### * chclust
>
> flush(stderr()); flush(stdout())
>
> ### Name: chclust
> ### Title: Constrained hierarchical clustering
> ### Aliases: chclust plot.chclust bstick.chclust
> ### Keywords: cluster hplot
>
> ### ** Examples
>
> data(RLGH)
> diss <- dist(sqrt(RLGH$spec/100)^2)
> clust <- chclust(diss)
> bstick.chclust(clust, 10)
Loading required package: vegan
Warning in library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE, :
there is no package called 'vegan'
Error in bstick.chclust(clust, 10) : could not find function "bstick"
Execution halted
### End snippet
The function bstick.chclust listed below loads the package vegan which contains
bstick.default.
bstick.chclust <- function(n, ng=10, plot=TRUE, ...) {
if (n$method != "coniss")
stop("bstick cannot display conslink results")
require(vegan)
disp <- rev(n$height)
tot.disp <- disp[1]
disp <- abs(diff(disp))
nobj <- length(n$height)
bs <- bstick(nobj, tot.disp)
yR <- range(disp[1:(ng-1)], bs[1:(ng-1)])
if (plot) {
plot(2:ng, disp[1:(ng-1)], type="o", ylim=yR, ylab="Sum of Squares", xlab
= "Number of groups")
lines(2:ng, bs[1:(ng-1)], col="red", type="o")
}
invisible(data.frame(nGroups = 2:(ng), dispersion=disp[1:(ng-1)], bstick =
bs[1:(ng-1)]))
}
vegan is included as a Suggests in the DESCRIPTION file and the package checks
OK on r-oldrel-macosx-ix86. It also checks OK with R 2.10.0 on OS X on my own
Mac. My code could be improved and I should probably trap the warning issued
by require, but I don't understand why vegan is not loading when checking on
CRAN. Any help will be gratefully received!
Many thanks, Steve
Steve Juggins
School of Geography, Politics & Sociology
Newcastle University Tel: +44 (0)191 222 8799
Newcastle upon Tyne Fax: +44 (0)191 222 5421
NE1 7RU, UK Mobile: +44 (0)7740054905
http://www.staff.ncl.ac.uk/staff/stephen.juggins/
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