From Simon.Urbanek at r-project.org  Mon Nov 16 15:32:21 2009
From: Simon.Urbanek at r-project.org (Simon Urbanek)
Date: Mon, 16 Nov 2009 09:32:21 -0500
Subject: [Rd] Problem building package for R 2.10.0 on Mac OS X
In-Reply-To: <alpine.OSX.1.00.0911151846230.80685@tystie.local>
References: <467931F038D8AC4F85B4CB76256781E1132717AC68@EXSAN03.campus.ncl.ac.uk>
	<alpine.OSX.1.00.0911151846230.80685@tystie.local>
Message-ID: <E1139B51-AAA7-4594-AC31-CC1258B07B28@r-project.org>

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/
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> -- 
> Brian D. Ripley,                  ripley at 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
>
>



[Rd] Problem building package for R 2.10.0 on Mac OS X
Simon Urbanek