• using R version 3.0.1 Patched (2013-05-16 r62757)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘TreePar/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘TreePar’ version ‘2.3’
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘TreePar’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over 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 namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... OK
• 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 examples ... ERROR
  Running examples in ‘TreePar-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: bdtypes.stt.lik
  > ### Title: bdtypes.stt.lik: calculates the likelihood of a tree under a
  > ### 2-type birth-death model.
  > ### Aliases: bdtypes.stt.lik
  >
  > ### ** Examples
  >
  > set.seed(1)
  > lambda11<-15
  > lambda12<-3
  > lambda21<-1
  > lambda22<-3
  > death1<-4
  > death2<-4
  > sampprob1<-0.05
  > sampprob2<-0.05
  > l<-rbind(c(lambda11,lambda12),c(lambda21,lambda22))
  > d<-c(death1,death2)
  > s<-c(sampprob1,sampprob2)
  > n<-20
  > init<- -1
  >
  > tree<-sim.bdtypes.stt.taxa(n,l,d,s,init)
  >
  > #Calculate likelihood for lambda11=15,lambda12=lambda21=lambda22=mu1=mu2=2,gamma=0
  > bdtypes.stt.lik(par=c(2,2,2,2),phylo=tree,fix=rbind(c(1,6,7,8),c(15,-5,0,0),c(1,1,1,1)),sampfrac=s,survival=0,posR=0)
  At line 1205 of file lsoda.f
  Fortran runtime error: Index '2' of dimension 1 of array 'y' above upper bound of 1