* using log directory 'E:/GIT/RBBGCMuso/RBBGCMuso.Rcheck'
* using R version 4.2.2 (2022-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using options '--no-manual --as-cran'
* checking for file 'RBBGCMuso/DESCRIPTION' ... OK
* this is package 'RBBGCMuso' version '0.7.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  inst/examples/hhs/cygwin1.dll
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for executable files ... WARNING
Found the following executable files:
  inst/examples/hhs/cygwin1.dll
  inst/examples/hhs/muso
  inst/examples/hhs/muso.exe
  inst/examples/hhs/muso7.0b7.exe
  inst/mtclim43
  inst/mtclim43.exe
Source packages should not contain undeclared executable files.
See section 'Package structure' in the 'Writing R Extensions' manual.
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking serialization versions ... OK
* checking whether package 'RBBGCMuso' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'changemulline(filename = epc[1], ': unused argument (filename = epc[1]) 
  Note: possible error in 'changemulline(filename = iniInput[1], ': unused argument (filename = iniInput[1]) 
  Note: possible error in 'musoDate(startYear = startYear, ': unused argument (corrigated = FALSE) 
  Note: possible error in 'changemulline(filePaths = basename(sourceEpc), ': unused arguments (fileOut = epcOut, fileToChange = "epc") 
  Note: possible error in 'musoDate(settings$startYear, ': unused argument (corrigated = FALSE) 
See 'E:/GIT/RBBGCMuso/RBBGCMuso.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* checking installed package size ... NOTE
  installed size is 13.4Mb
  sub-directories of 1Mb or more:
    examples  12.2Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'tcltk' 'rmarkdown'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Found the following non-empty subdirectories of 'inst' also used by R:
  inst/data
It is recommended not to interfere with package subdirectories used by
R.
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'Boruta' 'Rcpp' 'grDevices' 'graphics' 'ncdf4'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [14s] NOTE
File 'RBBGCMuso/R/atStart.R':
  .onLoad calls:
    cat(sprintf("This is RBBGCMuso version 1.0\nDefault Biome-BGCMuSo version: %d",     RMuso_version))

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

This is RBBGCMuso version 1.0
Default Biome-BGCMuSo version: 7agroLikelihood : <anonymous>: no visible global function definition for
  'dnorm'
calibrateMuso: no visible global function definition for 'lines'
calibrateMuso: no visible global function definition for 'polygon'
calibrateMuso: no visible global function definition for 'points'
checkMeteoBGC : sradAvgShortestDay: no visible global function
  definition for 'na.omit'
checkMeteoBGC : sradAvgLongestDay: no visible global function
  definition for 'na.omit'
corrigMuso: no visible global function definition for 'musoLeapYears'
createSoilFile : createMusoLayers: no visible binding for global
  variable '.'
multiSiteCalib : <anonymous>: no visible global function definition for
  'sd'
multiSiteCalib: no visible global function definition for 'svg'
multiSiteCalib: no visible global function definition for 'dev.off'
multiSiteCalib: no visible global function definition for 'lm'
multiSiteCalib: no visible global function definition for 'png'
multiSiteCalib: no visible global function definition for 'par'
musoGlue: no visible global function definition for 'quantile'
musoGlue : <anonymous>: no visible global function definition for
  'quantile'
musoGlue: no visible global function definition for 'pdf'
musoGlue: no visible global function definition for 'par'
musoGlue: no visible global function definition for 'abline'
musoGlue: no visible global function definition for 'dev.off'
musoMapping: no visible binding for global variable 'mMapping'
musoMonte: no visible binding for global variable 'procString'
musoQuickEffect: no visible binding for global variable 'parVal'
musoSensi : doSensi: no visible global function definition for 'lm'
musoSensi : doSensi: no visible binding for global variable 'var'
musoSensi : doSensi: no visible binding for global variable 'name'
normalMuso: possible error in changemulline(filename = epc[1],
  calibrationPar, parameters): unused argument (filename = epc[1])
normalMuso: possible error in changemulline(filename = iniInput[1],
  calibrationPar, parameters): unused argument (filename = iniInput[1])
plotMuso : <anonymous>: no visible binding for global variable
  'whereAmI'
plotMuso: possible error in musoDate(startYear = startYear, numYears =
  numberOfYears, combined = TRUE, corrigated = FALSE): unused argument
  (corrigated = FALSE)
plotMuso: possible error in musoDate(startYear = startYear, numYears =
  numberOfYears, combined = FALSE, corrigated = FALSE): unused argument
  (corrigated = FALSE)
plotMuso: no visible binding for global variable 'year'
plotMuso: no visible binding for global variable 'cum_yieldC_HRV'
plotMuso: no visible binding for global variable 'date2'
plotMuso : pointOrLineOrPlot: no visible binding for global variable
  '.'
plotMuso : pointOrLineOrPlot: no visible binding for global variable
  'outputs'
plotMuso : pointOrLineOrPlot: no visible binding for global variable
  'bla'
plotMusoWithData: no visible binding for global variable 'modIndex'
plotMusoWithData: no visible binding for global variable 'measuredData'
plotMusoWithData: no visible binding for global variable 'measured'
prepareFromAgroMo: no visible global function definition for 'reshape'
randEpc: possible error in changemulline(filePaths =
  basename(sourceEpc), calibrationPar = randVals[[1]], contents =
  randVals[[2]][i, ], fileOut = epcOut, fileToChange = "epc"): unused
  arguments (fileOut = epcOut, fileToChange = "epc")
rungetMuso: possible error in musoDate(settings$startYear,
  settings$numYears, corrigated = FALSE): unused argument (corrigated =
  FALSE)
setupMuso: no visible binding for global variable 'numDate'
spinupMuso: possible error in changemulline(filename = epc[1],
  calibrationPar, parameters): unused argument (filename = epc[1])
spinupMuso: possible error in changemulline(filename = iniInput[1],
  calibrationPar, parameters): unused argument (filename = iniInput[1])
spinupMuso: no visible binding for global variable 'EPCS'
spinupMuso : <anonymous>: no visible binding for global variable 'EPCS'
spinupMuso : <anonymous>: no visible binding for global variable
  'WRONGEPC'
truncNorm: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  . EPCS WRONGEPC abline bla cum_yieldC_HRV date2 dev.off dnorm lines
  lm mMapping measured measuredData modIndex musoLeapYears na.omit name
  numDate outputs par parVal pdf png points polygon procString quantile
  reshape rnorm sd svg var whereAmI year
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "png", "svg")
  importFrom("graphics", "abline", "lines", "par", "points", "polygon")
  importFrom("stats", "dnorm", "lm", "na.omit", "quantile", "reshape",
             "rnorm", "sd", "var")
to your NAMESPACE file.
* checking Rd files ... WARNING
./man/getSoilDataFull.Rd: non-ASCII input and no declared encoding
problem found in 'getSoilDataFull.Rd'
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'depTree'
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 'calibMuso':
calibMuso
  Code: function(settings = setupMuso(), calibrationPar = NULL,
                 parameters = NULL, outVars = NULL, timee = "d",
                 debugging = FALSE, logfilename = NULL, keepEpc =
                 FALSE, export = FALSE, silent = FALSE, aggressive =
                 FALSE, keepBinary = FALSE, binaryPlace = "./",
                 fileToChange = "epc", skipSpinup = TRUE,
                 modifyOriginal = FALSE, prettyOut = FALSE,
                 postProcString = NULL, doBackup = TRUE)
  Docs: function(settings, parameters = NULL, timee = "d", debugging =
                 FALSE, logfilename = NULL, keepEpc = FALSE, export =
                 FALSE, silent = FALSE, aggressive = FALSE, leapYear =
                 FALSE)
  Argument names in code not in docs:
    calibrationPar outVars keepBinary binaryPlace fileToChange
    skipSpinup modifyOriginal prettyOut postProcString doBackup
  Argument names in docs not in code:
    leapYear
  Mismatches in argument names (first 3):
    Position: 2 Code: calibrationPar Docs: parameters
    Position: 3 Code: parameters Docs: timee
    Position: 4 Code: outVars Docs: debugging
  Mismatches in argument default values:
    Name: 'settings' Code: setupMuso() Docs: 

Codoc mismatches from documentation object 'calibrateMuso':
calibrateMuso
  Code: function(measuredData, parameters = read.csv("parameters.csv",
                 stringsAsFactor = FALSE), startDate = NULL, endDate =
                 NULL, formatString = "%Y-%m-%d", dataVar, outLoc =
                 "./calib", preTag = "cal-", settings = setupMuso(),
                 outVars = NULL, iterations = 100, skipSpinup = TRUE,
                 plotName = "calib.jpg", modifyOriginal = TRUE,
                 likelihood, uncertainity = NULL, naVal = NULL,
                 postProcString = NULL, thread_prefix = "thread",
                 numCores = max(c(parallel::detectCores() - 1, 1)), pb
                 = txtProgressBar(min = 0, max = iterations, style =
                 3), maxLikelihoodEpc = TRUE, pbUpdate =
                 setTxtProgressBar, outputLoc = "./", method = "GLUE",
                 lg = FALSE, w = NULL, ...)
  Docs: function(measuredData, parameters = read.csv("parameters.csv",
                 stringsAsFactor = FALSE), startDate = NULL, endDate =
                 NULL, formatString = "%Y-%m-%d", dataVar, outLoc =
                 "./calib", preTag = "cal-", settings = setupMuso(),
                 outVars = NULL, iterations = 100, skipSpinup = TRUE,
                 plotName = "calib.jpg", modifyOriginal = TRUE,
                 likelihood, uncertainity = NULL, naVal = NULL,
                 postProcString = NULL, thread_prefix = "thread",
                 numCores = (parallel::detectCores() - 1), pb =
                 txtProgressBar(min = 0, max = iterations, style = 3),
                 maxLikelihoodEpc = TRUE, pbUpdate = setTxtProgressBar,
                 outputLoc = "./", method = "GLUE", lg = FALSE, w =
                 NULL, ...)
  Mismatches in argument default values:
    Name: 'numCores' Code: max(c(parallel::detectCores() - 1, 1)) Docs: (parallel::detectCores() - 1)

Codoc mismatches from documentation object 'musoMapping':
musoMapping
  Code: function(code, mapData =
                 getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]])
  Docs: function(code, mapData = NULL)
  Mismatches in argument default values:
    Name: 'mapData' Code: getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]] Docs: NULL

Codoc mismatches from documentation object 'musoMappingFind':
musoMapping
  Code: function(code, mapData =
                 getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]])
  Docs: function(code, mapData = NULL)
  Mismatches in argument default values:
    Name: 'mapData' Code: getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]] Docs: NULL

Codoc mismatches from documentation object 'normalMuso':
normalMuso
  Code: function(settings = NULL, parameters = NULL, timee = "d",
                 debugging = FALSE, logfilename = NULL, keepEpc =
                 FALSE, export = FALSE, silent = FALSE, aggressive =
                 FALSE, leapYear = FALSE, binaryPlace = NULL,
                 fileToChange = "epc", keepBinary = FALSE)
  Docs: function(settings, parameters = NULL, timee = "d", debugging =
                 FALSE, logfilename = NULL, keepEpc = FALSE, export =
                 FALSE, silent = FALSE, aggressive = FALSE, leapYear =
                 FALSE)
  Argument names in code not in docs:
    binaryPlace fileToChange keepBinary
  Mismatches in argument default values:
    Name: 'settings' Code: NULL Docs: 

Codoc mismatches from documentation object 'plotMuso':
plotMuso
  Code: function(settings = NULL, variable = "all", timee = "d", silent
                 = TRUE, calibrationPar = NULL, parameters = NULL,
                 debugging = FALSE, keepEpc = FALSE, fileToChange =
                 "epc", logfilename = NULL, aggressive = FALSE,
                 leapYear = FALSE, plotName = NULL, plotType = "cts",
                 layerPlot = FALSE, colour = "blue", skipSpinup = TRUE,
                 fromData = FALSE, timeFrame = "day", selectYear =
                 NULL, groupFun = mean, separateFile = FALSE, dpi =
                 300, postProcString = NULL)
  Docs: function(settings, variable, timee = "d", silent = TRUE,
                 debugging = FALSE, keepEpc = FALSE, logfilename =
                 NULL, aggressive = FALSE, leapYear = FALSE, export =
                 FALSE)
  Argument names in code not in docs:
    calibrationPar parameters fileToChange plotName plotType layerPlot
    colour skipSpinup fromData timeFrame selectYear groupFun
    separateFile dpi postProcString
  Argument names in docs not in code:
    export
  Mismatches in argument names (first 3):
    Position: 5 Code: calibrationPar Docs: debugging
    Position: 6 Code: parameters Docs: keepEpc
    Position: 7 Code: debugging Docs: logfilename
  Mismatches in argument default values:
    Name: 'settings' Code: NULL Docs: 
    Name: 'variable' Code: "all" Docs: 

Codoc mismatches from documentation object 'plotMusoWithData':
plotMuso
  Code: function(settings = NULL, variable = "all", timee = "d", silent
                 = TRUE, calibrationPar = NULL, parameters = NULL,
                 debugging = FALSE, keepEpc = FALSE, fileToChange =
                 "epc", logfilename = NULL, aggressive = FALSE,
                 leapYear = FALSE, plotName = NULL, plotType = "cts",
                 layerPlot = FALSE, colour = "blue", skipSpinup = TRUE,
                 fromData = FALSE, timeFrame = "day", selectYear =
                 NULL, groupFun = mean, separateFile = FALSE, dpi =
                 300, postProcString = NULL)
  Docs: function(settings, variable, timee = "d", silent = TRUE,
                 debugging = FALSE, keepEpc = FALSE, logfilename =
                 NULL, aggressive = FALSE, leapYear = FALSE, export =
                 FALSE)
  Argument names in code not in docs:
    calibrationPar parameters fileToChange plotName plotType layerPlot
    colour skipSpinup fromData timeFrame selectYear groupFun
    separateFile dpi postProcString
  Argument names in docs not in code:
    export
  Mismatches in argument names (first 3):
    Position: 5 Code: calibrationPar Docs: debugging
    Position: 6 Code: parameters Docs: keepEpc
    Position: 7 Code: debugging Docs: logfilename
  Mismatches in argument default values:
    Name: 'settings' Code: NULL Docs: 
    Name: 'variable' Code: "all" Docs: 

Codoc mismatches from documentation object 'runMuso':
calibMuso
  Code: function(settings = setupMuso(), calibrationPar = NULL,
                 parameters = NULL, outVars = NULL, timee = "d",
                 debugging = FALSE, logfilename = NULL, keepEpc =
                 FALSE, export = FALSE, silent = FALSE, aggressive =
                 FALSE, keepBinary = FALSE, binaryPlace = "./",
                 fileToChange = "epc", skipSpinup = TRUE,
                 modifyOriginal = FALSE, prettyOut = FALSE,
                 postProcString = NULL, doBackup = TRUE)
  Docs: function(settings, parameters = NULL, timee = "d", debugging =
                 FALSE, logfilename = NULL, keepEpc = FALSE, export =
                 FALSE, silent = FALSE, aggressive = FALSE, leapYear =
                 FALSE)
  Argument names in code not in docs:
    calibrationPar outVars keepBinary binaryPlace fileToChange
    skipSpinup modifyOriginal prettyOut postProcString doBackup
  Argument names in docs not in code:
    leapYear
  Mismatches in argument names (first 3):
    Position: 2 Code: calibrationPar Docs: parameters
    Position: 3 Code: parameters Docs: timee
    Position: 4 Code: outVars Docs: debugging
  Mismatches in argument default values:
    Name: 'settings' Code: setupMuso() Docs: 

Codoc mismatches from documentation object 'setupMuso':
setupMuso
  Code: function(executable = NULL, parallel = F, calibrationPar =
                 c(1), outputLoc = NULL, modelOutputs = NULL, inputLoc
                 = NULL, metInput = NULL, CO2Input = NULL, plantInput =
                 NULL, thinInput = NULL, mowInput = NULL, grazInput =
                 NULL, harvInput = NULL, plougInput = NULL, fertInput =
                 NULL, irrInput = NULL, nitInput = NULL, iniInput =
                 NULL, epcInput = NULL, mapData = NULL, leapYear =
                 FALSE, version = 6, doCopy = TRUE)
  Docs: function(executable = NULL, parallel = F, calibrationPar =
                 c(1), outputLoc = NULL, inputLoc = NULL, metInput =
                 NULL, CO2Input = NULL, plantInput = NULL, thinInput =
                 NULL, mowInput = NULL, grazInput = NULL, harvInput =
                 NULL, plougInput = NULL, fertInput = NULL, irrInput =
                 NULL, nitInput = NULL, iniInput = NULL, epcInput =
                 NULL)
  Argument names in code not in docs:
    modelOutputs mapData leapYear version doCopy
  Mismatches in argument names (first 3):
    Position: 5 Code: modelOutputs Docs: inputLoc
    Position: 6 Code: inputLoc Docs: metInput
    Position: 7 Code: metInput Docs: CO2Input

Codoc mismatches from documentation object 'spinupMuso':
spinupMuso
  Code: function(settings = NULL, parameters = NULL, debugging = FALSE,
                 logfilename = NULL, keepEpc = FALSE, silent = FALSE,
                 aggressive = FALSE, fileToChange = "epc")
  Docs: function(settings, parameters = NULL, debugging = FALSE,
                 logfilename = NULL, keepEpc = FALSE, silent = FALSE,
                 aggressive = FALSE)
  Argument names in code not in docs:
    fileToChange
  Mismatches in argument default values:
    Name: 'settings' Code: NULL Docs: 

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'calibMuso':
  'keepBinary' 'binaryPlace' 'fileToChange' 'skipSpinup' 'prettyOut'

Undocumented arguments in documentation object 'calibrateMuso'
  'measuredData' 'parameters' 'startDate' 'endDate' 'formatString'
  'dataVar' 'outLoc' 'preTag' 'settings' 'outVars' 'iterations'
  'skipSpinup' 'plotName' 'modifyOriginal' 'likelihood' 'uncertainity'
  'naVal' 'postProcString' 'thread_prefix' 'numCores' 'pb'
  'maxLikelihoodEpc' 'pbUpdate' 'outputLoc' 'method' 'lg' 'w' '...'

Undocumented arguments in documentation object 'changemulline'
  'filePaths' 'calibrationPar' 'contents' 'src' 'outFiles'

Undocumented arguments in documentation object 'checkFileSystem'
  'root'

Documented arguments not in \usage in documentation object 'checkMeteoBGC':
  'metFileName'

Undocumented arguments in documentation object 'compareCalibratedWithOriginal'
  'key' 'modOld' 'modNew' 'mes' 'likelihoods' 'alignIndexes'
  'musoCodeToIndex' 'nameGroupTable' 'groupFun'

Undocumented arguments in documentation object 'compareMuso'
  'skipSpinup' 'timeFrame'

Undocumented arguments in documentation object 'flatMuso'
  'execPath' 'd' 'outE'

Undocumented arguments in documentation object 'getFilePath'
  'fileType' 'execPath'
Documented arguments not in \usage in documentation object 'getFilePath':
  'filetype'

Undocumented arguments in documentation object 'getFilesFromIni'
  'execPath'

Undocumented arguments in documentation object 'multiSiteCalib'
  'measurements' 'constraints'
Documented arguments not in \usage in documentation object 'multiSiteCalib':
  'measuremets' 'contsraints'

Undocumented arguments in documentation object 'multiSiteThread'
  'measuredData' 'parameters' 'startDate' 'endDate' 'formatString'
  'calTable' 'dataVar' 'outLoc' 'outVars' 'iterations' 'skipSpinup'
  'plotName' 'modifyOriginal' 'likelihood' 'uncertainity' 'burnin'
  'naVal' 'postProcString' 'threadNumber' 'constraints' 'th'

Undocumented arguments in documentation object 'musoDate'
  'startYear' 'endYears' 'numYears' 'combined' 'leapYearHandling'
  'prettyOut'

Undocumented arguments in documentation object 'musoGlue'
  'presCalFile' 'w' 'delta' 'settings' 'parameters' 'lg'
Documented arguments not in \usage in documentation object 'musoGlue':
  'plotName'

Undocumented arguments in documentation object 'musoMappingFind'
  'code' 'mapData'
Documented arguments not in \usage in documentation object 'musoMappingFind':
  'variable'
Objects in \usage without \alias in documentation object 'musoMappingFind':
  'musoMapping'

Undocumented arguments in documentation object 'musoMonte'
  'outLoc' 'outVars' 'silent' 'skipSpinup' 'constrains' 'skipZero'
  'postProcString' 'modifyOut' '...'
Documented arguments not in \usage in documentation object 'musoMonte':
  'calibrationPar'

Undocumented arguments in documentation object 'musoQuickEffect'
  'calibrationPar' 'fileToChange' 'modifyOriginal' 'outVar' 'parName'
  'yearNum' 'year'
Documented arguments not in \usage in documentation object 'musoQuickEffect':
  'fileTochange'

Undocumented arguments in documentation object 'musoRand'
  'iterations' 'fileType' 'burnin'
Documented arguments not in \usage in documentation object 'musoRand':
  'iteration'

Undocumented arguments in documentation object 'musoSensi'
  'monteCarloFile' 'outLoc' 'outVars' 'outputFile' 'plotName'
  'plotTitle' 'skipZero' 'postProcString' 'modifyOut' 'dpi'
Documented arguments not in \usage in documentation object 'musoSensi':
  'calibrationPar'

Documented arguments not in \usage in documentation object 'normalMuso':
  'binaryPlace' 'fileToChange' 'keepBinary'

Undocumented arguments in documentation object 'optiMuso'
  'measuredData' 'dataVar' 'preTag' 'outVars' 'modifyOriginal'
  'uncertainity' 'naVal' 'postProcString' 'w' 'lg' 'parallel'
Documented arguments not in \usage in documentation object 'optiMuso':
  'measuredDataFile' 'sep' 'filterCol' 'filterVal' 'selVar' 'pretag'
  'calPar' 'constrains' 'leapYear'

Documented arguments not in \usage in documentation object 'plotMuso':
  'plotType' 'skipSpinup'

Undocumented arguments in documentation object 'plotMusoWithData'
  'timee' 'silent' 'debugging' 'keepEpc' 'logfilename' 'aggressive'
  'leapYear' 'export'
Documented arguments not in \usage in documentation object 'plotMusoWithData':
  'sep' 'savePlot' 'NACHAR' 'csvFile' 'calibrationPar' 'parameters'
Objects in \usage without \alias in documentation object 'plotMusoWithData':
  'plotMuso'

Undocumented arguments in documentation object 'randEpc'
  'iterations' 'constrains'
Documented arguments not in \usage in documentation object 'randEpc':
  'iteration'

Undocumented arguments in documentation object 'readObservedData'
  'inFile' 'naString' 'sep' 'leapYearHandling' 'convert.var'
  'convert.scalar' 'convert.fun' 'convert.file' 'filterCol' 'filterVal'
  'selVar'

Documented arguments not in \usage in documentation object 'runMuso':
  'keepBinary' 'binaryPlace' 'fileToChange' 'skipSpinup' 'prettyOut'
Objects in \usage without \alias in documentation object 'runMuso':
  'calibMuso'

Undocumented arguments in documentation object 'saveAllMusoPlots'
  'type' 'outFile' 'colour' 'skipSpinup'
Documented arguments not in \usage in documentation object 'saveAllMusoPlots':
  'destination'

Documented arguments not in \usage in documentation object 'setupMuso':
  'modelOutputs'

Undocumented arguments in documentation object 'updateMusoMapping'
  'dest' 'version'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... NOTE
Package vignette with placeholder title 'Vignette Title':
  'my-vignette.Rmd'
* checking re-building of vignette outputs ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 7 WARNINGs, 7 NOTEs