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SciViews log file (check_x86_64_linux)

Thu Aug 18 15:51:17 2016: Checking package SciViews (SVN revision 558) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/SciViews.Rcheck’
* using R version 3.3.1 Patched (2016-08-17 r71112)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘SciViews/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SciViews’ version ‘0.9-12’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Philippe Grosjean ’

Found the following (possibly) invalid URLs:
  URL: http://www.sciviews.org/SciViews-R
    From: DESCRIPTION
          inst/CITATION
    Status: 404
    Message: Not Found

The Title field starts with the package name.
The Title field should be in title case, current version then in title case:
‘SciViews GUI API - Main package’
‘SciViews GUI API - Main Package’

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 ‘SciViews’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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
Unexported objects imported by ':::' calls:
  ‘grDevices:::.smoothScatterCalcDensity’ ‘grDevices:::recordPalette’
  ‘stats:::.check_vars_numeric’ ‘stats:::biplot.default’
  ‘stats:::screeplot.default’
  See the note in ?`:::` about the use of this operator.
  Including base/recommended package(s):
  ‘grDevices’ ‘stats’
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  all. any. one.
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 ... WARNING
Found a .Internal call in the following function:
  ‘optDef’
with calls to .Internal functions
  ‘getOption’

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.

Found an obsolete/platform-specific call in the following functions:
  ‘devCopyPdf’ ‘devInteractive’
Found the platform-specific devices:
  ‘X11’ ‘quartz’ ‘windows’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.

In addition to the above warning(s), found the following notes:

as.intBase: no visible global function definition for ‘.Intern’
as.integerBase: no visible global function definition for ‘.Intern’
char: no visible global function definition for ‘.Intern’
charEscape: no visible global function definition for ‘.Intern’
charLower: no visible global function definition for ‘.Intern’
charMatch: no visible global function definition for ‘.Intern’
charPMatch: no visible global function definition for ‘.Intern’
charSubstr: no visible global function definition for ‘.Intern’
charSubstr<-: no visible global function definition for ‘.Intern’
charTrunc: no visible global function definition for ‘.Intern’
charUpper: no visible global function definition for ‘.Intern’
debugOnce: no visible global function definition for ‘.Intern’
devClose: no visible global function definition for ‘devCur’
devNext: no visible global function definition for ‘devCur’
devPrev: no visible global function definition for ‘devCur’
devSet: no visible global function definition for ‘devNext’
dirCreate: no visible global function definition for ‘.Intern’
encoding: no visible global function definition for ‘.Intern’
encoding<-: no visible global function definition for ‘.Intern’
encoding<-: no visible global function definition for ‘setEncoding’
envNew: no visible global function definition for ‘.Intern’
envParent: no visible global function definition for ‘.Intern’
envParent<-: no visible global function definition for ‘.Intern’
envProfile: no visible global function definition for ‘.Intern’
evalQuote: no visible global function definition for ‘.Intern’
fileAccess: no visible global function definition for ‘.Intern’
fileAppend: no visible global function definition for ‘.Intern’
fileChmod: no visible global function definition for ‘.Intern’
fileCopy: no visible global function definition for ‘.Intern’
fileCreate: no visible global function definition for ‘.Intern’
fileExists: no visible global function definition for ‘.Intern’
fileInfo: no visible global function definition for ‘.Intern’
fileLink: no visible global function definition for ‘.Intern’
fileRemove: no visible global function definition for ‘.Intern’
fileRename: no visible global function definition for ‘.Intern’
fileShow: no visible global function definition for ‘.Intern’
fileSymLink: no visible global function definition for ‘.Intern’
fileUMask: no visible global function definition for ‘.Intern’
isDebugged: no visible global function definition for ‘.Intern’
matchCall: no visible global function definition for ‘.Intern’
p0: no visible global function definition for ‘.Intern’
p_: no visible global function definition for ‘.Intern’
parentFrame: no visible global function definition for ‘.Intern’
setEncoding: no visible global function definition for ‘.Intern’
setEncoding: no visible global function definition for ‘setEncoding’
sysCall: no visible global function definition for ‘.Intern’
sysCalls: no visible global function definition for ‘.Intern’
sysFrame: no visible global function definition for ‘.Intern’
sysFrames: no visible global function definition for ‘.Intern’
sysFunction: no visible global function definition for ‘.Intern’
sysOnExit: no visible global function definition for ‘.Intern’
sysParent: no visible global function definition for ‘.Intern’
sysParents: no visible global function definition for ‘.Intern’
sysnFrame: no visible global function definition for ‘.Intern’
topEnv: no visible global function definition for ‘.Intern’
Undefined global functions or variables:
  .Intern devCur devNext setEncoding
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘!’ ‘%:%’ ‘%else%’ ‘@’ ‘@<-’ ‘Cols’ ‘E’ ‘Pi’ ‘Rows’ ‘all.’ ‘any.’
  ‘asFALSE’ ‘asTRUE’ ‘autoloadEnv’ ‘autoloaded’ ‘baseEnv’
  ‘baseNamespaceEnv’ ‘boxplotInternal’ ‘boxplotStats’ ‘clevelandplot’
  ‘cm2in’ ‘color2rgb’ ‘colorAdjust’ ‘colorBlues9’ ‘colorCm’
  ‘colorConvert’ ‘colorConvertRgb’ ‘colorDens’ ‘colorGray’ ‘colorGrey’
  ‘colorHeat’ ‘colorRainbow’ ‘colorRwb’ ‘colorRyg’ ‘colorTerrain’
  ‘colorTopo’ ‘contourplot’ ‘contours’ ‘coplotIntervals’ ‘debugOnce’
  ‘devBitmap’ ‘devBmp’ ‘devCapabilities’ ‘devCapture’ ‘devClose’
  ‘devCloseAll’ ‘devControl’ ‘devCopy’ ‘devCopyBitmap’ ‘devCopyEps’
  ‘devCopyNew’ ‘devCopyPdf’ ‘devCur’ ‘devFlush’ ‘devHold’
  ‘devHoldFlush’ ‘devInteractive’ ‘devJpeg’ ‘devList’ ‘devNew’
  ‘devNext’ ‘devPS’ ‘devPSCairo’ ‘devPSOpt’ ‘devPdf’ ‘devPdfCairo’
  ‘devPdfOpt’ ‘devPng’ ‘devPrev’ ‘devRecord’ ‘devReplay’ ‘devSave’
  ‘devSet’ ‘devSize’ ‘devSvg’ ‘devTiff’ ‘devXfig’ ‘dumpFrames’
  ‘emptyEnv’ ‘enum’ ‘envNew’ ‘envParent’ ‘envParent<-’ ‘envProfile’
  ‘evalLocal’ ‘evalParent’ ‘evalQuote’ ‘filledplot’ ‘fontCid’
  ‘fontType1’ ‘fontsEmbed’ ‘fontsPS’ ‘fontsPdf’ ‘getSnapshot’
  ‘globalEnv’ ‘ifElse’ ‘in2cm’ ‘isDebugged’ ‘isDevInteractive’
  ‘isEmpty’ ‘isFALSE’ ‘isNamespaceEnv’ ‘l’ ‘l__cm’ ‘layoutShow’
  ‘matchCall’ ‘names’ ‘nc’ ‘nclassFD’ ‘nclassScott’ ‘nclassSturges’
  ‘nr’ ‘onExit’ ‘one’ ‘one.’ ‘opt’ ‘optCheck’ ‘optDef’ ‘package’
  ‘parentFrame’ ‘playSnapshot’ ‘plotInternal’ ‘plotNew’ ‘plotOpt’
  ‘plotOptAll’ ‘plotWindowInternal’ ‘rangeExtend’ ‘screenClose’
  ‘screenDelete’ ‘screenSet’ ‘screenSplit’ ‘smoothPanel’ ‘smoothplot’
  ‘starplot’ ‘stemplot’ ‘stopIfNot’ ‘stripplot’ ‘sysCall’ ‘sysFrame’
  ‘sysFunction’ ‘sysOnExit’ ‘sysParent’ ‘sysParents’ ‘sysSource’
  ‘sysStatus’ ‘sysnFrame’ ‘tempEnv’ ‘timing’ ‘topEnv’ ‘xConvert’
  ‘x__cm2user’ ‘x__in2user’ ‘xyConvert’ ‘xyCoords’ ‘xy__cm2user’
  ‘xy__in2user’ ‘xyzCoords’ ‘yConvert’ ‘y__cm2user’ ‘y__in2user’
All user-level objects in a package 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 'file':
fileCopy
  Code: function(from, to, overwrite = recursive, recursive = FALSE,
                 copy.mode = TRUE, copy.date = FALSE)
  Docs: function(from, to, overwrite = recursive, recursive = FALSE,
                 copy.mode = TRUE)
  Argument names in code not in docs:
    copy.date

* checking Rd \usage sections ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [3s/4s] OK
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 2 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/SciViews.Rcheck/00check.log’
for details.


Run time: 48.78 seconds.