• using R version 3.3.1 (2016-06-21)
• using platform: x86_64-pc-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘MAR1/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘MAR1’ version ‘1.0’
• 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 ‘MAR1’ 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 ... NOTE
  'library' or 'require' call to ‘MARSS’ 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: ‘tcltk’
    These packages need to be imported from (in the NAMESPACE file)
    for when this namespace is loaded but not attached.
  Unexported object imported by a ':::' call: ‘MARSS:::is.diagonal’
    See the note in ?`:::` about the use of this operator.
• checking S3 generic/method consistency ... NOTE
  Found the following apparent S3 methods exported but not registered:
    plot.MAR
  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
  bestfit.search.exhaustive: no visible global function definition for
    ‘glm’
  bestfit.search.exhaustive: no visible global function definition for
    ‘AIC’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘tktoplevel’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘tkwm.geometry’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘tkwm.title’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘tklabel’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘ttkprogressbar’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘tkgrid’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘tkgrid.columnconfigure’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘tkconfigure’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘AIC’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘glm’
  bestfit.search.exhaustive.true: no visible global function definition
    for ‘tkdestroy’
  bestfit.search.random: no visible global function definition for
    ‘tclVar’
  bestfit.search.random: no visible global function definition for
    ‘tktoplevel’
  bestfit.search.random: no visible global function definition for
    ‘tkwm.geometry’
  bestfit.search.random: no visible global function definition for
    ‘tkwm.title’
  bestfit.search.random: no visible global function definition for
    ‘tklabel’
  bestfit.search.random: no visible global function definition for
    ‘ttkprogressbar’
  bestfit.search.random: no visible global function definition for
    ‘tkgrid’
  bestfit.search.random: no visible global function definition for
    ‘tkbutton’
  bestfit.search.random: no visible global function definition for
    ‘tkfont.create’
  bestfit.search.random : <anonymous>: no visible global function
    definition for ‘tclvalue<-’
  bestfit.search.random: no visible global function definition for
    ‘tkgrid.columnconfigure’
  bestfit.search.random: no visible global function definition for
    ‘tkconfigure’
  bestfit.search.random: no visible global function definition for
    ‘runif’
  bestfit.search.random: no visible global function definition for
    ‘tclvalue’
  bestfit.search.random: no visible global function definition for
    ‘tkdestroy’
  export.MAR: no visible global function definition for ‘write.table’
  export.MAR: no visible global function definition for ‘stack’
  export.MAR : write.results: no visible global function definition for
    ‘write.table’
  export.MAR : write.results: no visible global function definition for
    ‘stack’
  fun.restrict.BC: no visible global function definition for ‘tktoplevel’
  fun.restrict.BC: no visible global function definition for ‘tkwm.title’
  fun.restrict.BC: no visible global function definition for ‘tkframe’
  fun.restrict.BC: no visible global function definition for
    ‘tkfont.create’
  fun.restrict.BC: no visible global function definition for ‘tclVar’
  fun.restrict.BC: no visible global function definition for ‘tclvalue’
  fun.restrict.BC: no visible global function definition for ‘tkbutton’
  fun.restrict.BC: no visible global function definition for
    ‘tkconfigure’
  fun.restrict.BC : <anonymous>: no visible global function definition
    for ‘tclvalue<-’
  fun.restrict.BC: no visible global function definition for ‘tkbind’
  fun.restrict.BC: no visible global function definition for ‘tkgrid’
  fun.restrict.BC: no visible global function definition for ‘tklabel’
  fun.restrict.BC: no visible global function definition for
    ‘tkwm.geometry’
  fun.restrict.BC: no visible global function definition for
    ‘tkgrid.rowconfigure’
  fun.restrict.BC: no visible global function definition for ‘tkfocus’
  fun.restrict.BC: no visible global function definition for
    ‘tkwait.variable’
  fun.restrict.BC: no visible global function definition for ‘tkdestroy’
  fun.set.variables: no visible global function definition for
    ‘tktoplevel’
  fun.set.variables: no visible global function definition for
    ‘tkwm.geometry’
  fun.set.variables: no visible global function definition for
    ‘tkwm.title’
  fun.set.variables: no visible global function definition for ‘tkframe’
  fun.set.variables: no visible global function definition for
    ‘tkfont.create’
  fun.set.variables: no visible global function definition for ‘tkgrid’
  fun.set.variables: no visible global function definition for ‘tklabel’
  fun.set.variables: no visible global function definition for ‘tclVar’
  fun.set.variables: no visible global function definition for ‘tclvalue’
  fun.set.variables : func.1: no visible global function definition for
    ‘tclvalue<-’
  fun.set.variables: no visible global function definition for ‘tkbutton’
  fun.set.variables: no visible global function definition for
    ‘tkconfigure’
  fun.set.variables: no visible global function definition for
    ‘tkgrid.configure’
  fun.set.variables: no visible global function definition for
    ‘tkgrid.columnconfigure’
  fun.set.variables : <anonymous>: no visible global function definition
    for ‘tclvalue<-’
  fun.set.variables: no visible global function definition for ‘tkbind’
  fun.set.variables: no visible global function definition for
    ‘tkwait.variable’
  fun.set.variables: no visible global function definition for
    ‘tkdestroy’
  hist.MARtop: no visible global function definition for ‘dev.new’
  hist.MARtop: no visible global function definition for ‘hist’
  hist.MARtop: no visible global function definition for ‘points’
  plot.MAR: no visible global function definition for ‘par’
  plot.MAR: no visible global function definition for ‘layout’
  plot.MAR: no visible global function definition for ‘palette’
  plot.MAR: no visible global function definition for ‘barplot’
  plot.MAR: no visible global function definition for ‘abline’
  plot.MAR: no visible global function definition for ‘points’
  plot.MAR: no visible global function definition for ‘box’
  plot.MAR: no visible global function definition for ‘plot’
  plot.MAR: no visible global function definition for ‘text’
  plot.MAR: no visible global function definition for ‘dev.new’
  plot.MAR: no visible global function definition for ‘dev.set’
  plot.MAR: no visible global function definition for ‘dev.prev’
  plot.MARtop: no visible global function definition for ‘par’
  plot.MARtop: no visible global function definition for ‘layout’
  plot.MARtop: no visible global function definition for ‘palette’
  plot.MARtop: no visible global function definition for ‘barplot’
  plot.MARtop: no visible global function definition for ‘abline’
  plot.MARtop: no visible global function definition for ‘box’
  plot.MARtop: no visible global function definition for ‘plot’
  plot.MARtop: no visible global function definition for ‘text’
  prepare.data: no visible global function definition for ‘aggregate’
  prepare.data: no visible global function definition for ‘approx’
  prepare.data: no visible global function definition for ‘na.omit’
  prepare.data: no visible global function definition for ‘runif’
  prepare.data: no visible binding for global variable ‘sd’
  run.mar: no visible global function definition for ‘flush.console’
  ss.mar1: no visible global function definition for ‘MARSS’
  summary.MAR : make.coef.sum: no visible global function definition for
    ‘aggregate’
  Undefined global functions or variables:
    AIC MARSS abline aggregate approx barplot box dev.new dev.prev
    dev.set flush.console glm hist layout na.omit palette par plot points
    runif sd stack tclVar tclvalue tclvalue<- text tkbind tkbutton
    tkconfigure tkdestroy tkfocus tkfont.create tkframe tkgrid
    tkgrid.columnconfigure tkgrid.configure tkgrid.rowconfigure tklabel
    tktoplevel tkwait.variable tkwm.geometry tkwm.title ttkprogressbar
    write.table
  Consider adding
    importFrom("grDevices", "dev.new", "dev.prev", "dev.set", "palette")
    importFrom("graphics", "abline", "barplot", "box", "hist", "layout",
               "par", "plot", "points", "text")
    importFrom("stats", "AIC", "aggregate", "approx", "glm", "na.omit",
               "runif", "sd")
    importFrom("utils", "flush.console", "stack", "write.table")
  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 examples ... [3s/3s] OK
• checking PDF version of manual ... OK
• DONE

Status: 3 NOTEs