SCM

R Development Page

greenbrown log file (check_x86_64_linux)

Mon Mar  6 10:25:24 2017: Checking package greenbrown (SVN revision 96) ...
* using log directory ‘/mnt/building/build_2017-03-06-10-24/RF_PKG_CHECK/PKGS/greenbrown.Rcheck’
* using R version 3.3.3 RC (2017-02-28 r72286)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘greenbrown/DESCRIPTION’ ... OK
* this is package ‘greenbrown’ version ‘2.4.3’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Matthias Forkel , Thomas Wutzler ’

New submission

Strong dependencies not in mainstream repositories:
  phenopix
* 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 ‘greenbrown’ can be installed ... [9s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘trigger’
* 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 ':::' imports not declared from:
  ‘Rssa’ ‘ncdf’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AccuracyAssessment: no visible global function definition for
  ‘addmargins’
AllEqual: no visible global function definition for ‘na.omit’
AllTsteps: no visible global function definition for ‘time’
AnomaliesFiltersLags: no visible binding for global variable ‘median’
AnomaliesFiltersLags: no visible global function definition for
  ‘ts.union’
AnomaliesFiltersLags : .Filter: no visible global function definition
  for ‘ts.union’
AnomaliesFiltersLags : .Lags: no visible global function definition for
  ‘ts.union’
AnomaliesFiltersLags : .Lags: no visible global function definition for
  ‘lag’
ColorMatrix: no visible global function definition for ‘median’
ColorMatrix: no visible global function definition for ‘col2rgb’
ColorMatrix: no visible global function definition for ‘rgb’
CompareClassification: no visible global function definition for
  ‘na.omit’
CorrectDOY: no visible global function definition for ‘na.omit’
CorrectDOY: no visible global function definition for ‘median’
CorrectDOY: no visible global function definition for ‘IQR’
Decompose: no visible global function definition for ‘cycle’
Decompose: no visible global function definition for ‘frequency’
Decompose: no visible global function definition for ‘ts’
FillPermanentGaps: no visible global function definition for
  ‘frequency’
FitDoubleLogBeck : : no visible global function definition
  for ‘rnorm’
FitDoubleLogBeck : : no visible global function definition
  for ‘sd’
FitDoubleLogBeck: no visible binding for global variable ‘optim’
FitDoubleLogBeck: no visible global function definition for ‘optim’
FitDoubleLogBeck: no visible global function definition for ‘lm’
FitDoubleLogBeck: no visible global function definition for ‘coef’
FitDoubleLogBeck: no visible binding for global variable ‘var’
FitDoubleLogElmore : : no visible global function definition
  for ‘rnorm’
FitDoubleLogElmore : : no visible global function definition
  for ‘sd’
FitDoubleLogElmore: no visible binding for global variable ‘optim’
FitDoubleLogElmore: no visible global function definition for ‘optim’
FitDoubleLogElmore: no visible binding for global variable ‘var’
GetTsStatisticsRaster : GetTsStatistics: no visible global function
  definition for ‘lm’
GetTsStatisticsRaster : GetTsStatistics: no visible global function
  definition for ‘sd’
InterpolateMatrix: no visible global function definition for ‘lm’
IsPermanentGap: no visible global function definition for ‘frequency’
IsPermanentGap: no visible global function definition for ‘ts’
IsPermanentGap: no visible global function definition for ‘runmed’
IsPermanentGap: no visible global function definition for ‘stl’
IsPermanentGap: no visible global function definition for ‘tsp<-’
IsPermanentGap: no visible global function definition for ‘cycle’
KGE: no visible global function definition for ‘frequency’
KGE: no visible global function definition for ‘ts.union’
KGE: no visible global function definition for ‘na.omit’
KGE: no visible global function definition for ‘sd’
KGE: no visible global function definition for ‘cor’
KGERaster: no visible binding for global variable ‘sd’
KGETrendUncertainty: no visible global function definition for
  ‘ts.intersect’
KGETrendUncertainty: no visible global function definition for
  ‘frequency’
KGETrendUncertainty : : no visible global function
  definition for ‘window’
LmSeasonalCycle: no visible global function definition for ‘lm’
LmSeasonalCycle: no visible global function definition for ‘tsp<-’
LmSeasonalCycle: no visible global function definition for ‘tsp’
MannKendallSeg : : no visible global function definition for
  ‘time’
MannKendallSeg : : no visible global function definition for
  ‘ts’
MannKendallSeg : : no visible global function definition for
  ‘frequency’
MannKendallSeg : : no visible global function definition for
  ‘lm’
MannKendallSeg : : no visible global function definition for
  ‘coef’
MapBreakpoints: no visible global function definition for ‘hasArg’
MapBreakpoints: no visible global function definition for
  ‘colorRampPalette’
MapBreakpoints: no visible global function definition for ‘kmeans’
MapBreakpoints: no visible binding for global variable ‘median’
MeanSeasonalCycle: no visible global function definition for ‘cycle’
MeanSeasonalCycle: no visible global function definition for ‘start’
MeanSeasonalCycle: no visible global function definition for
  ‘frequency’
NoTrend: no visible global function definition for ‘time’
PhenoDeriv: no visible global function definition for ‘na.omit’
PhenoDeriv: no visible global function definition for ‘median’
PhenoTrs: no visible global function definition for ‘na.omit’
PhenoTrs: no visible global function definition for ‘median’
Phenology: no visible global function definition for ‘frequency’
Phenology: no visible global function definition for ‘ts’
PhenologyNCDF : : no visible global function definition for
  ‘ts’
PhenologyNCDF: no visible global function definition for ‘ts’
PhenologyRaster : .funForRaster: no visible global function definition
  for ‘ts’
PhenopixMY: no visible global function definition for ‘time’
PhenopixMY: no visible global function definition for ‘cycle’
PhenopixMY: no visible global function definition for ‘frequency’
PhenopixMY: no visible global function definition for ‘na.omit’
PhenopixMY : : no visible global function definition for
  ‘time’
PlotPhenCycle: no visible global function definition for ‘abline’
PlotPhenCycle: no visible global function definition for ‘segments’
PolygonNA: no visible global function definition for ‘median’
PolygonNA: no visible global function definition for ‘na.omit’
PolygonNA: no visible global function definition for ‘polygon’
SSASeasonalCycle: no visible global function definition for ‘start’
SSASeasonalCycle: no visible global function definition for ‘frequency’
SSASeasonalCycle: no visible global function definition for ‘approx’
SSASeasonalCycle: no visible global function definition for ‘time’
Seasonality: no visible global function definition for ‘par’
Seasonality: no visible global function definition for ‘spec.pgram’
Seasonality: no visible global function definition for ‘mtext’
Seasonality: no visible global function definition for ‘stl’
Seasonality: no visible global function definition for ‘cycle’
Seasonality: no visible global function definition for ‘time’
Seasonality: no visible global function definition for ‘lm’
Seasonality: no visible global function definition for ‘BIC’
Seasonality: no visible global function definition for ‘points’
Seasonality: no visible global function definition for ‘legend’
SimIAV: no visible global function definition for ‘rnorm’
SimIAV: no visible global function definition for ‘ts’
SimIAV: no visible global function definition for ‘median’
SimRem: no visible global function definition for ‘rnorm’
SimRem: no visible global function definition for ‘median’
SimRem: no visible global function definition for ‘ts’
SimSeas: no visible global function definition for ‘ts’
SimTrend: no visible global function definition for ‘ts’
SimTs: no visible global function definition for ‘ts’
SplitRasterEqually: no visible global function definition for ‘na.omit’
TSGFdoublelog: no visible global function definition for ‘frequency’
TSGFdoublelog: no visible global function definition for ‘ts’
TSGFlinear: no visible global function definition for ‘frequency’
TSGFlinear: no visible global function definition for ‘ts’
TSGFlinear: no visible global function definition for ‘runmed’
TSGFlinear: no visible global function definition for ‘window’
TSGFlinear: no visible global function definition for ‘approx’
TSGFlinear: no visible global function definition for ‘time’
TSGFphenopix: no visible global function definition for ‘frequency’
TSGFphenopix: no visible global function definition for ‘time’
TSGFphenopix: no visible global function definition for ‘window’
TSGFphenopix: no visible global function definition for ‘ts’
TSGFspline: no visible global function definition for ‘frequency’
TSGFspline: no visible global function definition for ‘ts’
TSGFspline: no visible global function definition for ‘smooth.spline’
TSGFspline: no visible global function definition for ‘time’
TSGFspline: no visible global function definition for ‘window’
TSGFssa: no visible global function definition for ‘frequency’
TSGFssa: no visible global function definition for ‘ts’
TSGFssa: no visible global function definition for ‘time’
TSGFssa: no visible global function definition for ‘rnorm’
TSGFstm: no visible global function definition for ‘frequency’
TSGFstm: no visible global function definition for ‘ts’
TSGFstm: no visible global function definition for ‘time’
Trend: no visible global function definition for ‘frequency’
TrendAAT: no visible global function definition for ‘frequency’
TrendAAT: no visible global function definition for ‘ts’
TrendAAT: no visible global function definition for ‘lm’
TrendAAT: no visible global function definition for ‘approx’
TrendAAT: no visible global function definition for ‘start’
TrendGradient: no visible global function definition for ‘na.omit’
TrendGradient : : no visible global function definition for
  ‘ts’
TrendPoly: no visible global function definition for ‘frequency’
TrendPoly: no visible global function definition for ‘ts’
TrendPoly: no visible global function definition for ‘lm’
TrendRQ: no visible global function definition for ‘approx’
TrendRQ: no visible global function definition for ‘ts’
TrendRQ: no visible global function definition for ‘start’
TrendRQ: no visible global function definition for ‘frequency’
TrendRQ: no visible global function definition for ‘coef’
TrendRaster : .funForRaster: no visible global function definition for
  ‘ts’
TrendRunmed: no visible global function definition for ‘frequency’
TrendRunmed: no visible global function definition for ‘ts’
TrendRunmed: no visible global function definition for ‘runmed’
TrendSSA: no visible global function definition for ‘frequency’
TrendSSA: no visible global function definition for ‘ts’
TrendSSA: no visible global function definition for ‘rnorm’
TrendSTL: no visible global function definition for ‘ts’
TrendSTL: no visible global function definition for ‘start’
TrendSTL: no visible global function definition for ‘end’
TrendSTL: no visible global function definition for ‘frequency’
TrendSTL: no visible global function definition for ‘rnorm’
TrendSTM: no visible global function definition for ‘lm’
TrendSTM: no visible global function definition for ‘BIC’
TrendSTM: no visible binding for global variable ‘na.pass’
TrendSTM: no visible global function definition for ‘ts’
TrendSTM: no visible global function definition for ‘start’
TrendSTM: no visible global function definition for ‘frequency’
TrendSTM: no visible global function definition for ‘approx’
TrendSTM: no visible global function definition for ‘time’
TrendSample: no visible global function definition for ‘frequency’
TrendSample : : no visible global function definition for
  ‘frequency’
TrendSample : : no visible global function definition for
  ‘window’
TrendSample: no visible global function definition for ‘wilcox.test’
TrendSeasonalAdjusted: no visible global function definition for ‘lm’
TrendSeasonalAdjusted: no visible global function definition for
  ‘approx’
TrendSeasonalAdjusted: no visible global function definition for ‘ts’
TrendSeasonalAdjusted: no visible global function definition for
  ‘start’
TrendSeasonalAdjusted: no visible global function definition for
  ‘frequency’
TrendSegmentsRaster: no visible global function definition for ‘ts’
TrendSegmentsRaster: no visible global function definition for ‘time’
TrendSegmentsRaster : .funForRaster: no visible global function
  definition for ‘na.omit’
TrendSpline: no visible global function definition for ‘frequency’
TrendSpline: no visible global function definition for ‘ts’
TrendSpline: no visible global function definition for ‘rnorm’
TrendSpline: no visible global function definition for ‘smooth.spline’
TrendUncertainty : : no visible global function definition
  for ‘time’
TrendUncertainty : : no visible global function definition
  for ‘ts’
TrendUncertainty : : no visible global function definition
  for ‘frequency’
TsPP : : no visible global function definition for ‘ts’
TsPP : : no visible global function definition for
  ‘frequency’
WriteNCDF4: no visible global function definition for ‘nc_create’
brgr.colors: no visible global function definition for
  ‘colorRampPalette’
plot.CompareClassification: no visible global function definition for
  ‘par’
plot.CompareClassification: no visible global function definition for
  ‘legend’
plot.Phenology: no visible global function definition for ‘frequency’
plot.PhenopixMY: no visible global function definition for ‘time’
plot.PhenopixMY: no visible global function definition for ‘palette’
plot.PhenopixMY: no visible global function definition for ‘abline’
plot.Trend: no visible global function definition for ‘axis’
plot.Trend: no visible global function definition for ‘points’
plot.Trend: no visible global function definition for ‘abline’
plot.Trend: no visible global function definition for ‘confint’
plot.Trend: no visible global function definition for ‘symnum’
plot.TrendGradient: no visible global function definition for ‘col2rgb’
plot.TrendGradient: no visible global function definition for ‘rgb’
plot.TrendGradient: no visible global function definition for ‘abline’
plot.TrendGradient: no visible global function definition for ‘polygon’
plot.TrendGradient: no visible global function definition for ‘symnum’
plot.TrendGradient: no visible global function definition for ‘points’
plot.TrendSample: no visible global function definition for ‘par’
plot.TrendSample: no visible global function definition for ‘segments’
plot.TrendSample: no visible global function definition for ‘abline’
plot.TrendSample: no visible global function definition for ‘points’
plot.TrendSample: no visible global function definition for ‘box’
plot.TrendSample: no visible global function definition for ‘symnum’
plot.TrendSample: no visible global function definition for ‘median’
print.Phenology: no visible global function definition for ‘sd’
print.Trend: no visible global function definition for ‘start’
print.Trend: no visible global function definition for ‘end’
Undefined global functions or variables:
  BIC IQR abline addmargins approx axis box coef col2rgb
  colorRampPalette confint cor cycle end frequency hasArg kmeans lag
  legend lm median mtext na.omit na.pass nc_create optim palette par
  points polygon rgb rnorm runmed sd segments smooth.spline spec.pgram
  start stl symnum time ts ts.intersect ts.union tsp tsp<- var
  wilcox.test window
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "palette",
             "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "mtext",
             "par", "points", "polygon", "segments")
  importFrom("methods", "hasArg")
  importFrom("stats", "BIC", "IQR", "addmargins", "approx", "coef",
             "confint", "cor", "cycle", "end", "frequency", "kmeans",
             "lag", "lm", "median", "na.omit", "na.pass", "optim",
             "rnorm", "runmed", "sd", "smooth.spline", "spec.pgram",
             "start", "stl", "symnum", "time", "ts", "ts.intersect",
             "ts.union", "tsp", "tsp<-", "var", "wilcox.test", "window")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following calls to data() loading into the global environment:
File ‘greenbrown/R/AnomaliesFiltersLags.R’:
  data(ndvi)
File ‘greenbrown/R/CompareClassification.R’:
  data(ndvimap)
File ‘greenbrown/R/Decompose.R’:
  data(ndvi)
File ‘greenbrown/R/FillPermanentGap.R’:
  data(ndvi)
  data(ndvi)
File ‘greenbrown/R/FitDoubleLogBeck.R’:
  data(ndvi)
File ‘greenbrown/R/FitDoubleLogElmore.R’:
  data(ndvi)
File ‘greenbrown/R/GetTsStatistics.R’:
  data(ndvimap)
File ‘greenbrown/R/KGE.R’:
  data(ndvi)
File ‘greenbrown/R/KGETrendUncertainty.R’:
  data(ndvi)
File ‘greenbrown/R/LmSeasonalCycle.R’:
  data(ndvi)
File ‘greenbrown/R/MannKendallSeg.R’:
  data(ndvi)
File ‘greenbrown/R/MapBreakpoints.R’:
  data(ndvimap)
File ‘greenbrown/R/MeanSeasonalCycle.R’:
  data(ndvi)
File ‘greenbrown/R/NamesTrendRaster.R’:
  data(ndvimap)
File ‘greenbrown/R/PhenoDeriv.R’:
  data(ndvi)
File ‘greenbrown/R/PhenoTrs.R’:
  data(ndvi)
File ‘greenbrown/R/Phenology.R’:
  data(ndvi)
File ‘greenbrown/R/PhenologyRaster.R’:
  data(ndvimap)
File ‘greenbrown/R/PlotPhenCycle.R’:
  data(ndvi)
File ‘greenbrown/R/TSGFdoublelog.R’:
  data(ndvi)
File ‘greenbrown/R/TSGFlinear.R’:
  data(ndvi)
File ‘greenbrown/R/TSGFphenopix.R’:
  data(ndvi)
File ‘greenbrown/R/TSGFspline.R’:
  data(ndvi)
File ‘greenbrown/R/TSGFstm.R’:
  data(ndvi)
File ‘greenbrown/R/Trend.R’:
  data(ndvi)
File ‘greenbrown/R/TrendAAT.R’:
  data(ndvi)
File ‘greenbrown/R/TrendClassification.R’:
  data(ndvimap)
File ‘greenbrown/R/TrendGradient.R’:
  data(ndvimap)
File ‘greenbrown/R/TrendLongestSEG.R’:
  data(ndvimap)
File ‘greenbrown/R/TrendPoly.R’:
  data(ndvi)
File ‘greenbrown/R/TrendRQ.R’:
  data(ndvi)
File ‘greenbrown/R/TrendRaster.R’:
  data(ndvimap)
File ‘greenbrown/R/TrendRunmed.R’:
  data(ndvi)
File ‘greenbrown/R/TrendSTL.R’:
  data(ndvi)
File ‘greenbrown/R/TrendSTM.R’:
  data(ndvi)
File ‘greenbrown/R/TrendSample.R’:
  data(ndvi)
File ‘greenbrown/R/TrendSeasonalAdjusted.R’:
  data(ndvi)
File ‘greenbrown/R/TrendSegmentsRaster.R’:
  data(ndvimap)
File ‘greenbrown/R/TrendSpline.R’:
  data(ndvi)
File ‘greenbrown/R/TrendUncertainty.R’:
  data(ndvi)
File ‘greenbrown/R/TsPP.R’:
  data(ndvi)
File ‘greenbrown/R/brgr.colors.R’:
  data(ndvimap)
File ‘greenbrown/R/phenopixMY.R’:
  data(ndvi)
File ‘greenbrown/R/plot.CompareClassification.R’:
  data(ndvimap)
File ‘greenbrown/R/plot.Phenology.R’:
  data(ndvi)
  data(ndvi)
File ‘greenbrown/R/plot.PhenopixMY.R’:
  data(ndvi)
File ‘greenbrown/R/plot.Trend.R’:
  data(ndvi)
  data(ndvi)
File ‘greenbrown/R/plot.TrendGradient.R’:
  data(ndvimap)
File ‘greenbrown/R/plot.TrendSample.R’:
  data(ndvi)
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... WARNING
greenbrown-package.Rd: non-ASCII input and no declared encoding
problem found in ‘greenbrown-package.Rd’
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'TrendSSA.Rd':
  ‘ssa’

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

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘MannKendallSeg’ ‘NoUnc’
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 ... 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 ... [34m/34m] OK
Examples with CPU or elapsed time > 5s
                               user system  elapsed
PhenologyRaster            1458.508 10.560 1469.246
Phenology                   137.316  0.392  137.713
TSGFdoublelog                92.228  0.008   92.241
TsPP                         73.612  0.004   73.616
TrendRaster                  36.864  0.000   36.864
TSGFphenopix                 25.136  0.004   25.139
plot.CompareClassification   23.120  0.008   23.129
CompareClassification        22.624  0.048   22.671
GetTsStatisticsRaster        15.756  0.008   15.765
NamesTrendRaster             13.720  0.004   13.726
TrendClassification          13.004  0.004   13.008
TrendSegmentsRaster          12.940  0.008   12.950
TrendLongestSEG              12.652  0.008   12.661
MapBreakpoints               12.528  0.012   12.539
FitDoubleLogBeck             11.444  0.000   11.447
brgr.colors                   9.680  0.004    9.683
Trend                         8.940  0.000    8.940
KGE                           5.724  0.000    5.726
TrendSeasonalAdjusted         5.556  0.004    5.558
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 3 NOTEs
See
  ‘/mnt/building/build_2017-03-06-10-24/RF_PKG_CHECK/PKGS/greenbrown.Rcheck/00check.log’
for details.


Run time: 2160.14 seconds.

Additional Logs:   00install.out
Thanks to:
Vienna University of Economics and Business University of Wisconsin - Madison Powered By FusionForge