Thanks, Brian, I was away traveling/away from Internet and all hell
breaks lose :) [more precisely Fortran broke for some reason].
Stephen,
in the case of rioja it is really a bug in your code - you have to
check the result of require() or "depend" on vegan. "Suggests" means
that your package works without those packages but can have improved
functionality with them. In your case the example breaks if you don't
have vegan - thus the package doesn't really work without vegan. (As
of why vegan is not there that is my problem ;)) Thanks for the
report, though.
Cheers,
Simon
On Nov 15, 2009, at 15:04 , Prof Brian Ripley wrote:
Please ask such questions on R-sig-mac, or directly to the Mac
package builder (Simon Urbanek).
As you will see from
http://cran.r-project.org/web/checks/check_summary.html
at least 150 packages are in the same boat (not building because
dependencies are missing), so something has gone wrong on the build
machine. There seem to be results for 'vegan', but they are for a
pre-release (2.10.0 alpha), not the released version.
Perhaps related, there have been no R-patched builds on
r.research.att.com for 'leopard' (the main R build for R 2.10.0)
since Nov 4.
Simon has been travelling, and will no doubt get to this when he has
time. Meanwhile, Mac users can fairly easily build packages from
the sources (provided they have installed Xcode), so this is not
something to fret about.
One point specific to Mac is that the distributed packages are tri-
architecture (i386, x86_64, ppc) and so need to work on all three
archs to get distributed (at least in principle). There have been
quite a few packages (including earlier versions of yours) that
failed on 64-bit platforms.
On Sun, 15 Nov 2009, Stephen Juggins wrote:
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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--
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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