R Development Page

REddyProc log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2017-03-13-08-44/RF_PKG_CHECK/PKGS/REddyProc.Rcheck'
* using R version 3.3.3 Patched (2017-03-06 r72327)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'REddyProc/DESCRIPTION' ... OK
* this is package 'REddyProc' version '1.0.0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Department for Biogeochemical Integration '

New submission

No package encoding and non-ASCII characters in the following R files:
  R/DataFunctions.R
    611:     ## 'Ta' - air temperature in C
    617:     ## 'Ts' - soil temperature in C
  R/EddyGapfilling.R
    415:     # Step 1: Look-up table (method 1) with window size 7 days
    417: 	# Step 2: Look-up table (method 1) with window size 14 days
    419:     # Step 3: Look-up table, Rg only (method 2) with window size 7 days, 
    423: 	# Step 5: Mean diurnal course (method 3) with window size 1, 2 days
    426:     # Step 6: Look-up table (method 1) with window size 21, 28, ..., 70   
    428:     # Step 7: Look-up table (method 2) with window size 14, 21, ..., 70  
    430:     # Step 8: Mean diurnal course (method 3) with window size 7, 14, ..., 210 days 

The Title field should be in title case, current version then in title case:
'Data processing and plotting utilities of (half-)hourly eddy-covariance measurements'
'Data Processing and Plotting Utilities of (Half-)Hourly Eddy-Covariance Measurements'

The Date field is over a month old.

Size of tarball: 17176573 bytes
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'REddyProc' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 92.0Mb
  sub-directories of 1Mb or more:
    examples  88.4Mb
    libs       1.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    '(Department for Biogeochemical Integration at MPI-BGC, Jena, Germany)'
  Authors@R: 'Markus Reichstein [aut], Antje Maria Moffat [aut, trl], Thomas Wutzler Wutzler [aut], Kerstin Sickel Sickel [aut, trl], Olaf Menzer Menzer [ctb], Mirco Migliavacca Migliavacca [cre]'

Maintainer field differs from that derived from Authors@R
  Maintainer: 'Department for Biogeochemical Integration '
  Authors@R:  'Mirco Migliavacca Migliavacca '

* checking top-level files ... NOTE
Files 'README.md' or 'NEWS.md' cannot be checked without 'pandoc' being installed.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Missing or unexported objects:
  'RNetCDF::att.get.nc' 'RNetCDF::close.nc' 'RNetCDF::dim.inq.nc'
  'RNetCDF::open.nc' 'RNetCDF::var.get.nc'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.bootStrapLRCFit: no visible global function definition for 'rnorm'
.estimateUStarSeason: no visible global function definition for 'cor'
.estimateUStarSeason: no visible global function definition for
  'recover'
.estimateUStarSeasonCPTSeveralT :  : : no visible
  global function definition for 'cor'
.fitSeg1: no visible global function definition for 'lm'
.fitSeg1: no visible global function definition for 'coef'
.fitSeg1: no visible global function definition for 'anova'
.fitSeg2: no visible global function definition for 'lm'
.fitSeg2: no visible global function definition for 'coef'
.fitSeg2: no visible global function definition for 'anova'
.optimLRC: no visible global function definition for 'quantile'
.optimLRC: no visible global function definition for 'median'
.optimLRC: no visible global function definition for 'optim'
.plotNEEVersusUStarTempClass: no visible global function definition for
  'plot'
.plotNEEVersusUStarTempClass: no visible global function definition for
  'adjustcolor'
.plotNEEVersusUStarTempClass: no visible global function definition for
  'quantile'
.plotNEEVersusUStarTempClass: no visible global function definition for
  'points'
.plotNEEVersusUStarTempClass: no visible global function definition for
  'abline'
.plotNEEVersusUStarTempClass: no visible global function definition for
  'legend'
fInterpolateGaps: no visible global function definition for 'approx'
fLoadEuroFlux16: no visible global function definition for 'read.csv'
fLoadEuroFlux16 : : no visible global function definition
  for 'read.csv'
fLoadTXTIntoDataframe: no visible global function definition for
  'read.csv'
fOptimSingleE0: no visible global function definition for 'nls'
fOptimSingleE0: no visible global function definition for 'resid'
fOptimSingleE0: no visible global function definition for 'quantile'
fOptimSingleE0: no visible global function definition for 'coef'
fOptimSingleE0 : : no visible global function definition for
  'recover'
fOptimSingleE0_Lev: no visible global function definition for 'resid'
fOptimSingleE0_Lev: no visible global function definition for
  'quantile'
fOptimSingleE0_Lev: no visible global function definition for 'coef'
fOptimSingleE0_Lev : : no visible global function definition
  for 'recover'
fWriteDataframeToFile: no visible global function definition for
  'write.table'
fillNAForward: no visible global function definition for 'median'
partGLEstimateTempSensInBoundsE0Only: no visible global function
  definition for 'median'
partGLEstimateTempSensInBoundsE0Only: no visible global function
  definition for 'nls'
partGLEstimateTempSensInBoundsE0Only: no visible global function
  definition for 'nls.control'
partGLEstimateTempSensInBoundsE0Only: no visible global function
  definition for 'coef'
partGLFitLRC: no visible global function definition for 'quantile'
partGLFitLRC: no visible global function definition for 'cov'
partGLFitLRCWindows: no visible global function definition for
  'quantile'
partGLFitNightRespRefOneWindow: no visible global function definition
  for 'lm'
partGLFitNightRespRefOneWindow: no visible global function definition
  for 'coef'
partGLSmoothTempSens : : no visible global function
  definition for 'capture.output'
partGLSmoothTempSens : : no visible global function
  definition for 'predict'
partGLSmoothTempSens : : no visible global function
  definition for 'quantile'
usEstUstarThreshold: no visible binding for global variable 'median'
usEstUstarThreshold: no visible global function definition for 'median'
usEstUstarThreshold: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  abline adjustcolor anova approx capture.output coef cor cov legend lm
  median nls nls.control optim plot points predict quantile read.csv
  recover resid rnorm write.table
Consider adding
  importFrom("grDevices", "adjustcolor")
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "anova", "approx", "coef", "cor", "cov", "lm",
             "median", "nls", "nls.control", "optim", "predict",
             "quantile", "resid", "rnorm")
  importFrom("utils", "capture.output", "read.csv", "recover",
             "write.table")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) RHLightResponseCostC.Rd:0-38: Must have a \description
checkRd: (5) whichValueGreaterEqualC.Rd:0-23: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'sEddyProc.example.Rd':
  \examples lines wider than 100 characters:
             EddyDataWithPosix.F <- fConvertTimeToPosix(EddyData.F, 'YDH', Year.s='Year', Day.s='DoY', Hour.s='Hour')
             EddyProc.C <- sEddyProc$new('DE-Tha', EddyDataWithPosix.F, c('NEE','Rg','Tair','VPD', 'Ustar'))
             EddyProc.C$sSetLocationInfo(Lat_deg.n=51.0, Long_deg.n=13.6, TimeZone_h.n=1)  #Location of DE-Tharandt
             EddyProc.C$sMDSGapFill('NEE', FillAll.b=TRUE) #Fill all values to estimate flux uncertainties
             EddyProc.C$sMDSGapFill('Rg', FillAll.b=FALSE) #Fill only the gaps for the meteo condition, e.g. 'Rg'
             EddyProc.C$sMDSGapFill('Tair', FillAll.b=FALSE)         # Gap-filled Tair (and NEE) needed for partitioning 
             EddyProc.C$sMDSGapFill('VPD', FillAll.b=FALSE)          # Gap-filled Tair (and NEE) needed for partitioning 
             #EddyProc.C$sGLFluxPartition(controlGLPart.l=partGLControl(isBoundLowerNEEUncertainty=FALSE))   # day time partitioning -> Reco ... [TRUNCATED]
             #plot( -EddyProc.C$sTEMP$GPP_DT + EddyProc.C$sTEMP$Reco_DT ~ EddyProc.C$sTEMP$NEE_f ); abline(0,1)
             #EddyProc.C$sMRFluxPartition(parsE0Regression=list(TempRange.n=2.0, optimAlgorithm="LM")        )  
             EddyProc.C <- sEddyProc$new('DE-Tha', EddyDataWithPosix.F, c('NEE','Rg','Tair','VPD', 'Ustar'))
             EddyProc.C$sSetLocationInfo(Lat_deg.n=51.0, Long_deg.n=13.6, TimeZone_h.n=1)  #Location of DE-Tharandt
             # Gapfilling by default it takes the annually aggregated estimate is used to mark periods with low uStar
             EddyProc.C$sMRFluxPartition(Lat_deg.n=51.0, Long_deg.n=13.6, TimeZone_h.n=1, Suffix.s='WithUstar')  # Note suffix
             EddyProc.C$sMRFluxPartition(Lat_deg.n=51.0, Long_deg.n=13.6, TimeZone_h.n=1, Suffix.s='WithUstar')  # Note suffix
             colnames(CombinedDataAmeriflux.F <- renameVariablesInDataframe(CombinedData.F, getBGC05ToAmerifluxVariableNameMapping() ))
             CombinedDataAmeriflux.F$TIMESTAMP_END <- POSIXctToBerkeleyJulianDate( EddyProc.C$sExportData()[[1]] )
             #colnames(tmp <- renameVariablesInDataframe(CombinedData.F, getAmerifluxToBGC05VariableNameMapping() ))
             EddySetups.C <- sEddyProc$new('DE-Tha', EddyDataWithPosix.F, c('NEE','Rg','Tair','VPD','Ustar'))
             EddySetups.C$sSetLocationInfo(Lat_deg.n=51.0, Long_deg.n=13.6, TimeZone_h.n=1)  #Location of DE-Tharandt
             EddySetups.C$sMDSGapFillAfterUstar('NEE', FillAll.b=FALSE, UstarThres.df=0.3, UstarSuffix.s='Thres1')
             EddySetups.C$sMDSGapFillAfterUstar('NEE', FillAll.b=FALSE, UstarThres.df=0.4, UstarSuffix.s='Thres2')
             EddySetups.C$sMDSGapFill('Tair', FillAll.b=FALSE)    # Gap-filled Tair needed for partitioning
             EddySetups.C$sMDSGapFill('VPD', FillAll.b=FALSE)    # Gap-filled VPD needed for daytime partitioning
             colnames(EddySetups.C$sExportResults()) # Note the suffix in output columns also of GPP, Reco, GPP_DT, and Reco_DT
             EddyTest.C$sSetLocationInfo(Lat_deg.n=51.0, Long_deg.n=13.6, TimeZone_h.n=1)  #Location of DE-Tharandt
             #+++ Gap fill variable with (non-default) variables and limits including preselection of data with quality flag QF==0 
             EddyTest.C$sMDSGapFill('LE', QFVar.s='QF', QFValue.n=0, V1.s='Rg', T1.n=30, V2.s='Tsoil', T2.n=2, 'Step', 0.1)
             #+++ Use individual gap filling subroutines with different window sizes and up to five variables and limits
             Result_Step1.F <- EddyTest.C$sFillLUT(3, 'Rg',50, 'rH',30, 'Tair',2.5, 'Tsoil',2, 'Step',0.5)
             EddyTest.C$sPlotHHFluxesY('VAR_fall', Year.i=1998) #Individual fill result columns are called 'VAR_...' 
             # Example 3 for advanced users: Explicit demonstration of MDS gap filling algorithm for filling NEE
             EddyTestMDS.C$sSetLocationInfo(Lat_deg.n=51.0, Long_deg.n=13.6, TimeZone_h.n=1)  #Location of DE-Tharandt
             for( WinDays.i in seq(21,70,7) ) Result_Step6.F <- EddyTestMDS.C$sFillLUT(WinDays.i, V1.s, T1.n, V2.s, T2.n, V3.s, T3.n)
             for( WinDays.i in seq(14,70,7) ) Result_Step7.F <- EddyTestMDS.C$sFillLUT(WinDays.i, V1.s, T1.n)
             EddySetups.C <- sEddyProc$new('DE-Tha', EddyDataWithPosix.F, c('NEE','Rg','Tair','VPD','Ustar'))
             EddySetups.C$sSetLocationInfo(Lat_deg.n=51.0, Long_deg.n=13.6, TimeZone_h.n=1)  #Location of DE-Tharandt
             # A version can be seen at https://github.com/bgctw/REddyProc/blob/master/vignettes/DEGebExample.md

Rd file 'sMDSGapFillAfterUStarDistr.Rd':
  \usage lines wider than 90 characters:
     sMDSGapFillAfterUStarDistr(..., UstarThres.df, UstarSuffix.V.s = colnames(UstarThres.df)[-1])

Rd file 'usEstUstarThreshold.Rd':
  \usage lines wider than 90 characters:
         ctrlUstarSub.l = usControlUstarSubsetting(), fEstimateUStarBinned = usEstUstarThresholdSingleFw2Binned, 

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'sEddyProc'
Undocumented data sets:
  'EddyData.F'
Undocumented S4 classes:
  'sEddyProc'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'sCalcPotRadiation' but not in code:
  sCalcPotRadiation

Functions or methods with usage in documentation object 'sEddyProc.new' but not in code:
  sEddyProc.new

Functions or methods with usage in documentation object 'sEstUstarThreshold' but not in code:
  sEstUstarThreshold

Functions or methods with usage in documentation object 'sEstUstarThresholdDistribution' but not in code:
  sEstUstarThresholdDistribution

Functions or methods with usage in documentation object 'sExportData' but not in code:
  sExportData

Functions or methods with usage in documentation object 'sExportResults' but not in code:
  sExportResults

Functions or methods with usage in documentation object 'sFillInit' but not in code:
  sFillInit

Functions or methods with usage in documentation object 'sFillLUT' but not in code:
  sFillLUT

Functions or methods with usage in documentation object 'sFillMDC' but not in code:
  sFillMDC

Functions or methods with usage in documentation object 'sGLFluxPartition' but not in code:
  sGLFluxPartition

Functions or methods with usage in documentation object 'sGetData' but not in code:
  sGetData

Functions or methods with usage in documentation object 'sMDSGapFill' but not in code:
  sMDSGapFill

Functions or methods with usage in documentation object 'sMDSGapFillAfterUStarDistr' but not in code:
  sMDSGapFillAfterUStarDistr

Functions or methods with usage in documentation object 'sMDSGapFillAfterUstar' but not in code:
  sMDSGapFillAfterUstar

Functions or methods with usage in documentation object 'sMRFluxPartition' but not in code:
  sMRFluxPartition

Functions or methods with usage in documentation object 'sPlotDailySums' but not in code:
  sPlotDailySums

Functions or methods with usage in documentation object 'sPlotDailySumsY' but not in code:
  sPlotDailySumsY

Functions or methods with usage in documentation object 'sPlotDiurnalCycle' but not in code:
  sPlotDiurnalCycle

Functions or methods with usage in documentation object 'sPlotFingerprint' but not in code:
  sPlotFingerprint

Functions or methods with usage in documentation object 'sPlotFingerprintY' but not in code:
  sPlotFingerprintY

Functions or methods with usage in documentation object 'sPlotHHFluxes' but not in code:
  sPlotHHFluxes

Functions or methods with usage in documentation object 'sPlotHHFluxesY' but not in code:
  sPlotHHFluxesY

Functions or methods with usage in documentation object 'sPlotNEEVersusUStarForSeason' but not in code:
  sPlotNEEVersusUStarForSeason

Functions or methods with usage in documentation object 'sPrintFrames' but not in code:
  sPrintFrames

Functions or methods with usage in documentation object 'sRegrE0fromShortTerm' but not in code:
  sRegrE0fromShortTerm

Functions or methods with usage in documentation object 'sRegrRref' but not in code:
  sRegrRref

Functions or methods with usage in documentation object 'sSetLocationInfo' but not in code:
  sSetLocationInfo

* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R' [75s]
 OK
** running tests for arch 'x64' ...
  Running 'doRUnit.R' [78s]
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 7 NOTEs
See
  'R:/run/building/build_2017-03-13-08-44/RF_PKG_CHECK/PKGS/REddyProc.Rcheck/00check.log'
for details.


Run time: 403.04 seconds.