R cmd check

Many items of documentation are documented as "TODO".  These need to be fixed

Passes more check() stuff now.  Still have some packages/namespace issues to square away.

Remaining things to fix:
```
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'datadr' 'lattice' 'base64enc' 'knitr' 'markdown' 'shiny' 'digest'
  'codetools' 'hexbin' 'ggplot2' 'jsonlite' 'fastICA'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data                2.0Mb
    trelliscopeViewer   2.3Mb

* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  'Cairo' 'httpuv'
'library' or 'require' calls not declared from:
  'data.table' 'grid'
'library' or 'require' calls to packages already attached by Depends:
  'base64enc' 'datadr' 'digest' 'ggplot2' 'lattice' 'shiny'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'base64enc' 'codetools' 'datadr' 'digest' 'fastICA' 'ggplot2'
  'hexbin' 'jsonlite' 'knitr' 'lattice' 'markdown' '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 '::':
  'codetools:::findGlobals' 'httpuv:::startServer'
  'httpuv:::stopServer'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'codetools:::collectUsageHandlers' 'lattice:::calculateGridLayout'
  'lattice:::compute.layout' 'lattice:::evaluate.legend'
  'lattice:::getLabelList' 'lattice:::grobFromLabelList'
  'shiny:::callAppHook' 'shiny:::file.path.ci' 'shiny:::handlerManager'
  'shiny:::p_randomInt' 'shiny:::serviceApp'
  'shiny:::setShowcaseDefault' 'shiny:::shinyCallingHandlers'
  'shiny:::startApp' 'shiny:::workerId'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.

* checking R code for possible problems ... NOTE
addDisplay: no visible binding for global variable 'verbose'
findDisplay: no visible binding for global variable 'displayListDF'
getCogInfo: no visible binding for global variable 'type'
getCognostics : <anonymous>: no visible global function definition for
  'getCognosticsSub'
listDisplays: no visible binding for global variable 'displayListDF'
mongoSaveCognostics: no visible global function definition for
  'vdbMongoInit'
myRunApp: no visible binding for global variable
  '.shinyServerMinVersion'
nbDisplay: no visible binding for global variable 'displayList'
nbDisplayList : <anonymous>: no visible binding for global variable
  'displayList'
oldGetCurCogDat.data.frame: no visible global function definition for
  'logMsg'
oldGetCurCogDat.mongoCogDatConn: no visible global function definition
  for 'logMsg'
removeDisplay: no visible binding for global variable
  'displayListNames'
syncLocalData: no visible binding for global variable 'displayListDF'
syncLocalData: no visible binding for global variable 'dataClass'
```