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permute log file (check_x86_64_linux)

Thu Aug 18 15:09:43 2016: Checking package permute (SVN revision 2847) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/permute.Rcheck’
* using R version 3.3.1 Patched (2016-08-17 r71112)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘permute/DESCRIPTION’ ... OK
* this is package ‘permute’ version ‘0.8-3’
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Gavin L. Simpson ’

Insufficient package version (submitted: 0.8.3, existing: 0.9.0)

The Title field should be in title case, current version then in title case:
‘Functions for generating restricted permutations of data’
‘Functions for Generating Restricted Permutations of Data’

The Date field is not in ISO 8601 yyyy-mm-dd format.
* 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 ‘permute’ can be installed ... [2s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
doShuffle: no visible global function definition for ‘runif’
doShuffleSet: no visible global function definition for ‘runif’
how: no visible global function definition for ‘getCall’
permuplot: no visible global function definition for ‘par’
permuplot : xy.series: no visible global function definition for
  ‘xy.coords’
permuplot : xy.free: no visible global function definition for ‘runif’
permuplot : xy.free: no visible global function definition for
  ‘xy.coords’
permuplot : xy.grid: no visible global function definition for
  ‘xy.coords’
permuplot: no visible global function definition for ‘n2mfrow’
permuplot: no visible global function definition for ‘xy.coords’
permuplot: no visible global function definition for ‘strheight’
permuplot: no visible global function definition for ‘strwidth’
permuplot: no visible global function definition for ‘plot.new’
permuplot: no visible global function definition for ‘plot.window’
permuplot: no visible global function definition for ‘polygon’
permuplot: no visible global function definition for ‘text’
permuplot: no visible global function definition for ‘box’
permuplot: no visible global function definition for ‘title’
setPlots<-.how: no visible global function definition for ‘getCall’
setStrata<-.Plots: no visible global function definition for ‘getCall’
setStrata<-.how: no visible global function definition for ‘getCall’
setWithin<-.how: no visible global function definition for ‘getCall’
shuffle: no visible global function definition for ‘update’
shuffle2: no visible global function definition for ‘runif’
shuffleGrid: no visible global function definition for ‘runif’
shuffleSeries: no visible global function definition for ‘runif’
shuffleSet2: no visible global function definition for ‘runif’
update.Plots: no visible global function definition for ‘getCall’
update.how: no visible global function definition for ‘getCall’
Undefined global functions or variables:
  box getCall n2mfrow par plot.new plot.window polygon runif strheight
  strwidth text title update xy.coords
Consider adding
  importFrom("grDevices", "n2mfrow", "xy.coords")
  importFrom("graphics", "box", "par", "plot.new", "plot.window",
             "polygon", "strheight", "strwidth", "text", "title")
  importFrom("stats", "getCall", "runif", "update")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘permute-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check
> ### Title: Utility functions for permutation schemes
> ### Aliases: check print.check print.summary.check summary.check
> ### Keywords: utilities design methods
> 
> ### ** Examples
> 
> ## use example data from ?pyrifos in package vegan
> require(vegan)
Loading required package: vegan
Failed with error:  ‘package ‘permute’ 0.8.3 is loaded, but >= 0.9.0 is required by ‘vegan’’
> example(pyrifos)
Warning in example(pyrifos) : no help found for ‘pyrifos’
> 
> ## Demonstrate the maximum number of permutations for the pyrifos data
> ## under a series of permutation schemes
> 
> ## no restrictions - lots of perms
> CONTROL <- how(within = Within(type = "free"))
> (check1 <- check(pyrifos, CONTROL))
Error in check(pyrifos, CONTROL) : object 'pyrifos' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(permute)
  > 
  > ## Runs the tests in inst/tests
  > test_package("permute")
  Error in eval(expr, envir, enclos) : 
    could not find function "library_if_available"
  Calls: test_package ... with_reporter -> force -> source_file -> eval -> eval
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  
  DONE ===========================================================================
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [10s/16s] OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/permute.Rcheck/00check.log’
for details.

Run time: 58.45 seconds.

Additional Logs:   00install.out
Thanks to:
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