* using log directory 'd:/Rcompile/CRANpkg/local/2.12/maticce.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'maticce/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'maticce' version '0.9-2'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'maticce' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: regimeMatrix.Rd:33-35: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... ERROR
Running examples in 'maticce-Ex.R' failed
The error most likely occurred in:

> ### Name: carex
> ### Title: Carex section Ovales tree, chromosome data, and nodes
> ### Aliases: carex
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   data(carex)
>   # tree comes in in phylo format, but we need an ouchtree object
>   trees <- lapply(carex$ovales.bayesTrees[1:10], ape2ouch) 
>   # for expedience, only tests for changes at up to 2 of the first 4 nodes on 10 trees visited in the MCMC phylogenetic analysis
>   trialBayesTrees <- runBatchHansen(trees, carex$ovales.data, carex$ovales.nodes[1:4], maxNodes = 2) 
Running regime 1
Error in length(sqrt.alpha) : 'sqrt.alpha' is missing
Calls: runBatchHansen -> batchHansen -> hansen
Execution halted