* using log directory 'd:/Rcompile/CRANpkg/local/3.3/RADami.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'RADami/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RADami' version '1.0-3'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'RADami' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ape::complement' by 'Biostrings::complement' when loading 'RADami'
See 'd:/Rcompile/CRANpkg/local/3.3/RADami.Rcheck/00install.out' for details.
* 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 use of S3 registration ... OK
* checking 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 ... NOTE
consensus.pyRAD: no visible global function definition for
  'write.table'
locus.dist: no visible global function definition for 'as.dist'
match.lnL.to.trees: no visible global function definition for
  'read.delim'
plot.locus.dist: no visible global function definition for 'layout'
plot.locus.dist: no visible global function definition for 'plot'
plot.locus.dist: no visible global function definition for 'points'
plot.locus.dist: no visible global function definition for 'text'
plot.locus.dist: no visible global function definition for 'segments'
plot.partitionedRAD: no visible global function definition for 'pdf'
plot.partitionedRAD: no visible global function definition for 'layout'
plot.partitionedRAD: no visible global function definition for 'plot'
plot.partitionedRAD: no visible global function definition for 'points'
plot.partitionedRAD: no visible global function definition for 'lm'
plot.partitionedRAD: no visible global function definition for
  'predict'
plot.partitionedRAD: no visible global function definition for 'lines'
plot.partitionedRAD: no visible global function definition for
  'matplot'
plot.partitionedRAD: no visible global function definition for
  'dev.off'
plot.rankedPartitionedRAD: no visible global function definition for
  'pdf'
plot.rankedPartitionedRAD: no visible global function definition for
  'layout'
plot.rankedPartitionedRAD: no visible global function definition for
  'plot'
plot.rankedPartitionedRAD: no visible global function definition for
  'points'
plot.rankedPartitionedRAD: no visible global function definition for
  'lm'
plot.rankedPartitionedRAD: no visible global function definition for
  'predict'
plot.rankedPartitionedRAD: no visible global function definition for
  'lines'
plot.rankedPartitionedRAD: no visible global function definition for
  'matplot'
plot.rankedPartitionedRAD: no visible global function definition for
  'dev.off'
Undefined global functions or variables:
  as.dist dev.off layout lines lm matplot pdf plot points predict
  read.delim segments text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "layout", "lines", "matplot", "plot", "points",
             "segments", "text")
  importFrom("stats", "as.dist", "lm", "predict")
  importFrom("utils", "read.delim", "write.table")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in 'RADami-Ex.R' failed
The error most likely occurred in:

> ### Name: genTrees
> ### Title: Generate permuted trees using rNNI or rtree, and check for
> ###   uniqueness.
> ### Aliases: genTrees
> 
> ### ** Examples
> 
>   data(oak.tree)
>   out <- genTrees(oak.tree, N = 10, maxmoves = 2, perms = c(5, 5))
Warning in if (perms == "DEFAULT") perms <- c(length(nni(x)), max(1, as.integer(N -  :
  the condition has length > 1 and only the first element will be used
doing maxmoves 1
doing maxmoves 2
Warning in c.multiPhylo(treeset, lapply(unique(rNNI(x, i, perms[i] * 1.5)),  :
  some objects not of class "phylo" or "multiPhylo": argument recursive=TRUE ignored
Error in UseMethod("unroot") : 
  no applicable method for 'unroot' applied to an object of class "list"
Calls: genTrees -> lapply -> FUN
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE