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sdmo log file (check_x86_64_linux)

Thu Mar 31 08:45:19 2016: Checking package sdmo (SVN revision 21) ...
* using log directory ‘/mnt/building/build_2016-03-31-08-44/RF_PKG_CHECK/PKGS/sdmo.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 ‘sdmo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sdmo’ version ‘0.0-12’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Babak Naimi ’
New submission

The Title field should be in title case, current version then in title case:
‘Species Distribution Modelling (old version)’
‘Species Distribution Modelling (Old Version)’

The Description field should start with a capital letter.

The Date field is over a month old.
* 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 ‘sdmo’ can be installed ... [4s/4s] 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘gbm’ ‘kernlab’ ‘leaflet’ ‘mgcv’ ‘randomForest’ ‘shiny’ ‘shinyBS’
  ‘shinythemes’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.brtFit: no visible binding for global variable ‘gbm’
.brtPredict: no visible binding for global variable ‘predict.gbm’
.gamFit: no visible binding for global variable ‘gam’
.rfFit: no visible binding for global variable ‘randomForest’
.svmFit: no visible binding for global variable ‘ksvm’
gui,ANY: no visible global function definition for ‘shinyApp’
gui,ANY: no visible global function definition for ‘fluidPage’
gui,ANY: no visible global function definition for ‘shinytheme’
gui,ANY: no visible global function definition for ‘HTML’
gui,ANY: no visible global function definition for ‘sidebarPanel’
gui,ANY: no visible global function definition for ‘bsCollapsePanel’
gui,ANY: no visible global function definition for ‘radioButtons’
gui,ANY: no visible global function definition for ‘selectizeInput’
gui,ANY: no visible global function definition for ‘hr’
gui,ANY: no visible global function definition for ‘br’
gui,ANY: no visible global function definition for ‘checkboxGroupInput’
gui,ANY: no visible global function definition for ‘numericInput’
gui,ANY: no visible global function definition for ‘sliderInput’
gui,ANY: no visible global function definition for ‘bsToggleButton’
gui,ANY: no visible global function definition for ‘mainPanel’
gui,ANY: no visible global function definition for ‘h3’
gui,ANY: no visible global function definition for ‘textOutput’
gui,ANY: no visible global function definition for ‘tabsetPanel’
gui,ANY: no visible global function definition for ‘tabPanel’
gui,ANY: no visible global function definition for ‘plotOutput’
gui,ANY: no visible global function definition for ‘verbatimTextOutput’
gui,ANY: no visible global function definition for ‘leafletOutput’
gui,ANY: no visible global function definition for ‘p’
gui,ANY: no visible global function definition for ‘actionButton’
gui,ANY : : no visible global function definition for
  ‘observe’
gui,ANY : : no visible global function definition for
  ‘updateSelectizeInput’
gui,ANY : : no visible global function definition for
  ‘reactive’
gui,ANY : : no visible global function definition for
  ‘readShapeSpatial’
gui,ANY : : no visible global function definition for
  ‘renderText’
gui,ANY : : no visible global function definition for
  ‘renderPrint’
gui,ANY : : no visible global function definition for
  ‘renderPlot’
gui,ANY : : no visible global function definition for
  ‘renderLeaflet’
gui,ANY : : no visible global function definition for ‘%>%’
gui,ANY : : no visible global function definition for
  ‘leaflet’
gui,ANY : : no visible global function definition for
  ‘addTiles’
gui,ANY : : no visible global function definition for
  ‘addMarkers’
sdmSetting,missing-speciesData-character : .local: no visible binding
  for global variable ‘models’
sdmSetting,missing-speciesData-character : .local: no visible binding
  for global variable ‘replication.type’
* checking Rd files ... WARNING
sdmData.Rd: non-ASCII input and no declared encoding
sdmSetting.Rd: non-ASCII input and no declared encoding
problems found in ‘sdmData.Rd’, ‘sdmSetting.Rd’
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'predict.Rd':
  \usage lines wider than 90 characters:
     predict(object, newdata, filename="", models,species=1,scenario,mean=FALSE,overwrite=TRUE, ...)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'read.sdm.Rd':
  ‘[sdm]{write.sdm}’ ‘[sdm]{sdm}’

Missing link or links in documentation object 'write.sdm.Rd':
  ‘[sdm]{read.sdm}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘cv.folds’ ‘thresholds’
Undocumented S4 classes:
  ‘numericORnull’
Undocumented S4 methods:
  generic 'thresholds' and siglist 'sdmEvaluate'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'sdmData':
sdmData
  Code: function(train, predictors, formula, test, filename, crs,
                 pseudo, size)
  Docs: function(train, predictors, formula, test, filename, crs)
  Argument names in code not in docs:
    pseudo size

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [2s/4s] OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 5 NOTEs
See
  ‘/mnt/building/build_2016-03-31-08-44/RF_PKG_CHECK/PKGS/sdmo.Rcheck/00check.log’
for details.


Run time: 86.83 seconds.