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biomod2 log file (check_x86_64_linux)

Mon Mar 13 16:05:32 2017: Checking package biomod2 (SVN revision 729) ...
* using log directory ‘/mnt/building/build_2017-03-13-16-04/RF_PKG_CHECK/PKGS/biomod2.Rcheck’
* using R version 3.3.3 Patched (2017-03-06 r72315)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘biomod2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomod2’ version ‘3.3-15’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Damien Georges ’

The Date field is over a month old.
* 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 ‘biomod2’ can be installed ... [12s/12s] OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    external   3.9Mb
* 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
tuning.maxent : tune: possible error in maxent(x, p, args =
  maxent.args[[i]], factors = categoricals, path = tmpfolder): unused
  arguments (args = maxent.args[[i]], factors = categoricals, path =
  tmpfolder)
* 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 ... WARNING
Undocumented arguments in documentation object 'BIOMOD_tuning'
  ‘occ’ ‘env’ ‘pres’ ‘bg’ ‘bg.coords’ ‘occ.grp’ ‘bg.grp’ ‘method’
  ‘maxent.args’ ‘args.lab’ ‘categoricals’ ‘aggregation.factor’ ‘kfolds’
  ‘bin.output’ ‘clamp’ ‘rasterPreds’ ‘parallel’ ‘numCores’ ‘RMvalues’
  ‘fc’
Documented arguments not in \usage in documentation object 'BIOMOD_tuning':
  ‘data’ ‘models’ ‘models.options’ ‘trControl’ ‘ctrl.GAM’ ‘ctrl.GBM’
  ‘ctrl.GLM’ ‘ctrl.CTA’ ‘ctrl.RF’ ‘ctrl.ANN’ ‘ctrl.MARS’ ‘ctrl.FDA’
  ‘metric’ ‘metric.ME’ ‘tuneLength’ ‘method.RF’ ‘method.ANN’
  ‘method.MARS’ ‘method.GAM’ ‘method.GLM’ ‘type.GLM’ ‘interaction.GLM’
  ‘cvmethod.ME’ ‘kfolds.ME’ ‘overlap.ME’ ‘clamp.ME’ ‘n.bg.ME’ ‘env.ME’
  ‘size.tune.ANN’ ‘decay.tune.ANN’ ‘maxit.ANN’ ‘MaxNWts.ANN’
  ‘parallel.ME’ ‘numCores.ME’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [30s/30s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/mnt/building/build_2017-03-13-16-04/RF_PKG_CHECK/PKGS/biomod2.Rcheck/00check.log’
for details.


Run time: 192.68 seconds.