R Development Page

tlocoh.dev log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2018-02-12-00-05/RF_PKG_CHECK/PKGS/tlocoh.dev.Rcheck'
* using R version 3.4.3 Patched (2018-02-03 r74238)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'tlocoh.dev/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tlocoh.dev' version '1.34.00'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Andy Lyons '

New submission

Version contains leading zeroes (1.34.00)

Strong dependencies not in mainstream repositories:
  tlocoh

The Title field should be in title case, current version then in title case:
'Development package for tlocoh'
'Development Package for Tlocoh'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages suggested but not available for checking: 'gpclib' 'leaflet'
* 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 'tlocoh.dev' can be installed ... 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 ... WARNING
'::' or ':::' import not declared from: 'rgeos'
'loadNamespace' or 'requireNamespace' call not declared from: 'rgeos'
'library' or 'require' calls to packages already attached by Depends:
  'pbapply' 'sp'
  Please remove these calls from your code.
'library' or 'require' call to 'leaflet' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'shiny'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'tlocoh:::clean_slivers' 'tlocoh:::vectorize.parameter'
  See the note in ?`:::` about the use of this operator.
Missing object imported by a ':::' call: 'shiny:::validateSelected'
Unexported objects imported by ':::' calls:
  'shiny:::choicesWithNames' 'shiny:::controlLabel'
  'shiny:::firstChoice' 'shiny:::selectOptions' 'shiny:::selectizeIt'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... WARNING
plot:
  function(x, ...)
plot.locoh.tumap:
  function(tumap, breaks, nsv, mnlv, ivg, legend, ...)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  plot.locoh.tumap
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
draw.polygons: no visible global function definition for 'dev.cur'
draw.polygons: no visible global function definition for 'rainbow'
draw.polygons: no visible global function definition for
  'flush.console'
draw.polygons: no visible global function definition for 'col2rgb'
draw.polygons: no visible global function definition for 'rgb'
draw.polygons: no visible global function definition for 'polygon'
draw.polygons: no visible global function definition for 'bringToTop'
gridlayer: no visible global function definition for 'error'
gridlayer: no visible global function definition for 'points'
hexlayer: no visible global function definition for 'error'
hexlayer: no visible global function definition for 'points'
iso2raster: no visible global function definition for 'is'
iso2raster: no visible global function definition for 'txtProgressBar'
iso2raster: no visible global function definition for
  'setTxtProgressBar'
iso2raster: no visible global function definition for 'rasterize'
iso2raster: no visible global function definition for 'cellStats'
iso2raster: no visible global function definition for 'par'
iso2raster: no visible global function definition for 'n2mfrow'
isodata.plot: no visible global function definition for 'is'
isodata.plot: no visible global function definition for 'rainbow'
isodata.plot: no visible global function definition for 'png'
isodata.plot: no visible global function definition for 'par'
isodata.plot: no visible global function definition for 'n2mfrow'
isodata.plot: no visible global function definition for 'matplot'
isodata.plot: no visible global function definition for 'text'
isodata.plot: no visible global function definition for 'dev.off'
lhs.bg.rast: no visible binding for global variable 'x'
lhs.exp.isodata: no visible global function definition for
  'flush.console'
lhs.iso.overlap: no visible global function definition for 'combn'
lhs.iso.overlap: no visible global function definition for
  'flush.console'
lhs.iso.overlap: no visible global function definition for
  'txtProgressBar'
lhs.iso.overlap: no visible global function definition for
  'setTxtProgressBar'
lhs.iso.overlap: no visible global function definition for 'is'
lhs.iso.overlap: no visible global function definition for
  'unionSpatialPolygons'
lhs.iso.rast: no visible global function definition for 'flush.console'
lhs.revisit.add: no visible global function definition for
  'flush.console'
lhs.shiny.select: no visible global function definition for 'shinyApp'
lhs.shiny.select: no visible global function definition for 'fluidPage'
lhs.shiny.select: no visible global function definition for 'fluidRow'
lhs.shiny.select: no visible global function definition for 'column'
lhs.shiny.select: no visible global function definition for
  'radioButtons'
lhs.shiny.select: no visible global function definition for
  'sliderInput'
lhs.shiny.select: no visible global function definition for 'div'
lhs.shiny.select: no visible global function definition for
  'actionLink'
lhs.shiny.select: no visible global function definition for 'icon'
lhs.shiny.select: no visible global function definition for
  'selectInput'
lhs.shiny.select: no visible global function definition for
  'plotOutput'
lhs.shiny.select: no visible global function definition for 'br'
lhs.shiny.select: no visible global function definition for 'p'
lhs.shiny.select: no visible global function definition for 'strong'
lhs.shiny.select: no visible global function definition for
  'checkboxInput'
lhs.shiny.select: no visible global function definition for
  'textOutput'
lhs.shiny.select: no visible binding for global variable 'tags'
lhs.shiny.select: no visible global function definition for
  'checkboxGroupInput'
lhs.shiny.select: no visible global function definition for
  'numericInput'
lhs.shiny.select: no visible global function definition for
  'actionButton'
lhs.shiny.select : : no visible global function definition
  for 'renderPlot'
lhs.shiny.select : : no visible global function definition
  for 'abline'
lhs.shiny.select : : no visible global function definition
  for 'observe'
lhs.shiny.select : : no visible global function definition
  for 'updateSelectInput'
lhs.shiny.select : : no visible global function definition
  for 'isolate'
lhs.shiny.select : : no visible global function definition
  for 'updateSliderInput'
lhs.shiny.select : : no visible global function definition
  for 'stopApp'
lhs.shiny.select: no visible global function definition for 'runApp'
lhs.so.add: no visible global function definition for 'flush.console'
lhs.to.add: no visible global function definition for 'flush.console'
lhs.to.stats: no visible global function definition for 'flush.console'
lhs.to.stats: no visible global function definition for 'as'
lhs.to.stats: no visible global function definition for 'runif'
lhs.to.stats: no visible global function definition for 'hist'
lhs.to.stats: no visible global function definition for 'par'
lhs.to.stats: no visible global function definition for 'n2mfrow'
lhs.to.stats: no visible global function definition for 'png'
lhs.to.stats: no visible global function definition for 'lines'
lhs.to.stats: no visible global function definition for 'text'
lhs.to.stats: no visible global function definition for 'dev.off'
lhs.to.stats: no visible global function definition for 't.test'
lhs.to.stats: no visible global function definition for 'ks.test'
lxy.explore: no visible global function definition for 'flush.console'
lxy.explore: no visible global function definition for '%>%'
lxy.explore: no visible global function definition for 'as'
lxy.explore: no visible global function definition for 'topo.colors'
lxy.explore: no visible global function definition for 'rainbow'
lxy.explore: no visible global function definition for
  'addCircleMarkers'
lxy.lhs.batch: no visible global function definition for
  'flush.console'
lxy.tumap: no visible global function definition for 'error'
lxy.tumap: no visible global function definition for 'flush.console'
lxy.tumap: no visible global function definition for 'as'
plot.locoh.tumap: no visible global function definition for 'hsv'
plot.locoh.tumap: no visible global function definition for 'box'
selectInputFlex: no visible binding for global variable 'tags'
selectInputFlex: no visible global function definition for 'div'
selectInputFlex: no visible global function definition for
  'validateCssUnit'
Undefined global functions or variables:
  %>% abline actionButton actionLink addCircleMarkers as box br
  bringToTop cellStats checkboxGroupInput checkboxInput col2rgb column
  combn dev.cur dev.off div error fluidPage fluidRow flush.console hist
  hsv icon is isolate ks.test lines matplot n2mfrow numericInput
  observe p par plotOutput png points polygon radioButtons rainbow
  rasterize renderPlot rgb runApp runif selectInput setTxtProgressBar
  shinyApp sliderInput stopApp strong t.test tags text textOutput
  topo.colors txtProgressBar unionSpatialPolygons updateSelectInput
  updateSliderInput validateCssUnit x
Consider adding
  importFrom("grDevices", "bringToTop", "col2rgb", "dev.cur", "dev.off",
             "hsv", "n2mfrow", "png", "rainbow", "rgb", "topo.colors")
  importFrom("graphics", "abline", "box", "hist", "lines", "matplot",
             "par", "points", "polygon", "text")
  importFrom("methods", "as", "is")
  importFrom("stats", "ks.test", "runif", "t.test")
  importFrom("utils", "combn", "flush.console", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 'gridlayer'
  'bbox' 'proj4string' 'mindim' 'cellsize' 'plotme' 'status'

Undocumented arguments in documentation object 'hexlayer'
  'bbox' 'proj4string' 'mindim' 'cellsize' 'plotme' 'status'

Undocumented arguments in documentation object 'lxy.sval.get'
  'ptsh'
Documented arguments not in \usage in documentation object 'lxy.sval.get':
  'The'

Undocumented arguments in documentation object 'lxy.tumap'
  'status'
Documented arguments not in \usage in documentation object 'lxy.tumap':
  'stats'

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.
S3 methods shown with full name in documentation object 'plot.locoh.tumap':
  'plot.locoh.tumap'

The \usage entries for S3 methods should use the \method markup and not
their full name.
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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  'R:/run/building/build_2018-02-12-00-05/RF_PKG_CHECK/PKGS/tlocoh.dev.Rcheck/00check.log'
for details.


Run time: 54.15 seconds.