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vegan log file (check_x86_64_linux)

Mon Apr  4 09:53:50 2016: Checking package vegan (SVN revision 2997) ...
* using log directory ‘/mnt/building/build_2016-04-04-09-44/RF_PKG_CHECK/PKGS/vegan.Rcheck’
* using R version 3.2.4 Patched (2016-03-28 r70390)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘vegan/DESCRIPTION’ ... OK
* this is package ‘vegan’ version ‘2.3-5’
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: ‘Jari Oksanen ’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 ‘vegan’ can be installed ... [10s/10s] 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
Found the following assignments to the global environment:
File ‘vegan/R/orditkplot.R’:
  assign(dumpName, xy, envir = .GlobalEnv)
  assign(dumpName, xy, envir = .GlobalEnv)
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘cclust’, ‘bipartite’, ‘vegan3d’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [43s/43s] OK
** found \donttest examples: check also with --run-donttest
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
   ‘decision-vegan.Rnw’ ... [2s/2s] OK
   ‘diversity-vegan.Rnw’ ... [3s/3s] OK
   ‘intro-vegan.Rnw’ ... [5s/5s] OK
   ‘partitioning.Rnw’ ... [2s/2s] OK
   ‘FAQ-vegan.Rmd’ using ‘UTF-8’ ... [0s/0s] OK
 [13s/13s] OK
* checking re-building of vignette outputs ... [13s/16s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/mnt/building/build_2016-04-04-09-44/RF_PKG_CHECK/PKGS/vegan.Rcheck/00check.log’
for details.


Run time: 274.15 seconds.

Additional Logs:   00install.out
Thanks to:
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