549 lines
26 KiB
Plaintext
549 lines
26 KiB
Plaintext
* using log directory 'E:/GIT/RBBGCMuso/RBBGCMuso.Rcheck'
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* using R version 4.2.2 (2022-10-31 ucrt)
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* using platform: x86_64-w64-mingw32 (64-bit)
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* using session charset: UTF-8
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* using options '--no-manual --as-cran'
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* checking for file 'RBBGCMuso/DESCRIPTION' ... OK
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* this is package 'RBBGCMuso' version '0.7.1'
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* checking package namespace information ... OK
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* checking package dependencies ... NOTE
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Imports includes 22 non-default packages.
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Importing from so many packages makes the package vulnerable to any of
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them becoming unavailable. Move as many as possible to Suggests and
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use conditionally.
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* checking if this is a source package ... NOTE
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Found the following apparent object files/libraries:
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inst/examples/hhs/cygwin1.dll
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Object files/libraries should not be included in a source package.
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* checking if there is a namespace ... OK
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* checking for executable files ... WARNING
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Found the following executable files:
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inst/examples/hhs/cygwin1.dll
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inst/examples/hhs/muso
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inst/examples/hhs/muso.exe
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inst/examples/hhs/muso7.0b7.exe
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inst/mtclim43
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inst/mtclim43.exe
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Source packages should not contain undeclared executable files.
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See section 'Package structure' in the 'Writing R Extensions' manual.
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* checking for hidden files and directories ... OK
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* checking for portable file names ... OK
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* checking serialization versions ... OK
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* checking whether package 'RBBGCMuso' can be installed ... WARNING
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Found the following significant warnings:
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Note: possible error in 'changemulline(filename = epc[1], ': unused argument (filename = epc[1])
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Note: possible error in 'changemulline(filename = iniInput[1], ': unused argument (filename = iniInput[1])
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Note: possible error in 'musoDate(startYear = startYear, ': unused argument (corrigated = FALSE)
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Note: possible error in 'changemulline(filePaths = basename(sourceEpc), ': unused arguments (fileOut = epcOut, fileToChange = "epc")
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Note: possible error in 'musoDate(settings$startYear, ': unused argument (corrigated = FALSE)
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See 'E:/GIT/RBBGCMuso/RBBGCMuso.Rcheck/00install.out' for details.
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Information on the location(s) of code generating the 'Note's can be
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obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
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to 'yes'.
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* checking installed package size ... NOTE
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installed size is 13.4Mb
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sub-directories of 1Mb or more:
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examples 12.2Mb
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* checking package directory ... OK
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* checking for future file timestamps ... OK
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* checking 'build' directory ... OK
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* checking DESCRIPTION meta-information ... NOTE
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Packages listed in more than one of Depends, Imports, Suggests, Enhances:
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'tcltk' 'rmarkdown'
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A package should be listed in only one of these fields.
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* checking top-level files ... OK
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* checking for left-over files ... OK
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* checking index information ... OK
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* checking package subdirectories ... WARNING
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Found the following non-empty subdirectories of 'inst' also used by R:
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inst/data
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It is recommended not to interfere with package subdirectories used by
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R.
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* checking R files for non-ASCII characters ... OK
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* checking R files for syntax errors ... OK
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* checking whether the package can be loaded ... OK
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* checking whether the package can be loaded with stated dependencies ... OK
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* checking whether the package can be unloaded cleanly ... OK
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* checking whether the namespace can be loaded with stated dependencies ... OK
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* checking whether the namespace can be unloaded cleanly ... OK
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* checking loading without being on the library search path ... OK
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* checking dependencies in R code ... NOTE
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Namespaces in Imports field not imported from:
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'Boruta' 'Rcpp' 'grDevices' 'graphics' 'ncdf4'
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All declared Imports should be used.
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* checking S3 generic/method consistency ... OK
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* checking replacement functions ... OK
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* checking foreign function calls ... OK
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* checking R code for possible problems ... [14s] NOTE
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File 'RBBGCMuso/R/atStart.R':
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.onLoad calls:
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cat(sprintf("This is RBBGCMuso version 1.0\nDefault Biome-BGCMuSo version: %d", RMuso_version))
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Package startup functions should use 'packageStartupMessage' to
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generate messages.
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See section 'Good practice' in '?.onAttach'.
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This is RBBGCMuso version 1.0
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Default Biome-BGCMuSo version: 7agroLikelihood : <anonymous>: no visible global function definition for
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'dnorm'
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calibrateMuso: no visible global function definition for 'lines'
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calibrateMuso: no visible global function definition for 'polygon'
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calibrateMuso: no visible global function definition for 'points'
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checkMeteoBGC : sradAvgShortestDay: no visible global function
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definition for 'na.omit'
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checkMeteoBGC : sradAvgLongestDay: no visible global function
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definition for 'na.omit'
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corrigMuso: no visible global function definition for 'musoLeapYears'
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createSoilFile : createMusoLayers: no visible binding for global
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variable '.'
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multiSiteCalib : <anonymous>: no visible global function definition for
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'sd'
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multiSiteCalib: no visible global function definition for 'svg'
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multiSiteCalib: no visible global function definition for 'dev.off'
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multiSiteCalib: no visible global function definition for 'lm'
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multiSiteCalib: no visible global function definition for 'png'
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multiSiteCalib: no visible global function definition for 'par'
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musoGlue: no visible global function definition for 'quantile'
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musoGlue : <anonymous>: no visible global function definition for
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'quantile'
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musoGlue: no visible global function definition for 'pdf'
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musoGlue: no visible global function definition for 'par'
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musoGlue: no visible global function definition for 'abline'
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musoGlue: no visible global function definition for 'dev.off'
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musoMapping: no visible binding for global variable 'mMapping'
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musoMonte: no visible binding for global variable 'procString'
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musoQuickEffect: no visible binding for global variable 'parVal'
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musoSensi : doSensi: no visible global function definition for 'lm'
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musoSensi : doSensi: no visible binding for global variable 'var'
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musoSensi : doSensi: no visible binding for global variable 'name'
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normalMuso: possible error in changemulline(filename = epc[1],
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calibrationPar, parameters): unused argument (filename = epc[1])
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normalMuso: possible error in changemulline(filename = iniInput[1],
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calibrationPar, parameters): unused argument (filename = iniInput[1])
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plotMuso : <anonymous>: no visible binding for global variable
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'whereAmI'
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plotMuso: possible error in musoDate(startYear = startYear, numYears =
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numberOfYears, combined = TRUE, corrigated = FALSE): unused argument
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(corrigated = FALSE)
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plotMuso: possible error in musoDate(startYear = startYear, numYears =
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numberOfYears, combined = FALSE, corrigated = FALSE): unused argument
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(corrigated = FALSE)
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plotMuso: no visible binding for global variable 'year'
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plotMuso: no visible binding for global variable 'cum_yieldC_HRV'
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plotMuso: no visible binding for global variable 'date2'
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plotMuso : pointOrLineOrPlot: no visible binding for global variable
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'.'
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plotMuso : pointOrLineOrPlot: no visible binding for global variable
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'outputs'
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plotMuso : pointOrLineOrPlot: no visible binding for global variable
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'bla'
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plotMusoWithData: no visible binding for global variable 'modIndex'
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plotMusoWithData: no visible binding for global variable 'measuredData'
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plotMusoWithData: no visible binding for global variable 'measured'
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prepareFromAgroMo: no visible global function definition for 'reshape'
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randEpc: possible error in changemulline(filePaths =
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basename(sourceEpc), calibrationPar = randVals[[1]], contents =
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randVals[[2]][i, ], fileOut = epcOut, fileToChange = "epc"): unused
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arguments (fileOut = epcOut, fileToChange = "epc")
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rungetMuso: possible error in musoDate(settings$startYear,
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settings$numYears, corrigated = FALSE): unused argument (corrigated =
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FALSE)
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setupMuso: no visible binding for global variable 'numDate'
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spinupMuso: possible error in changemulline(filename = epc[1],
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calibrationPar, parameters): unused argument (filename = epc[1])
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spinupMuso: possible error in changemulline(filename = iniInput[1],
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calibrationPar, parameters): unused argument (filename = iniInput[1])
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spinupMuso: no visible binding for global variable 'EPCS'
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spinupMuso : <anonymous>: no visible binding for global variable 'EPCS'
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spinupMuso : <anonymous>: no visible binding for global variable
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'WRONGEPC'
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truncNorm: no visible global function definition for 'rnorm'
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Undefined global functions or variables:
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. EPCS WRONGEPC abline bla cum_yieldC_HRV date2 dev.off dnorm lines
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lm mMapping measured measuredData modIndex musoLeapYears na.omit name
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numDate outputs par parVal pdf png points polygon procString quantile
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reshape rnorm sd svg var whereAmI year
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Consider adding
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importFrom("grDevices", "dev.off", "pdf", "png", "svg")
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importFrom("graphics", "abline", "lines", "par", "points", "polygon")
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importFrom("stats", "dnorm", "lm", "na.omit", "quantile", "reshape",
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"rnorm", "sd", "var")
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to your NAMESPACE file.
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* checking Rd files ... WARNING
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./man/getSoilDataFull.Rd: non-ASCII input and no declared encoding
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problem found in 'getSoilDataFull.Rd'
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* checking Rd metadata ... OK
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* checking Rd line widths ... OK
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* checking Rd cross-references ... OK
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* checking for missing documentation entries ... WARNING
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Undocumented data sets:
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'depTree'
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All user-level objects in a package should have documentation entries.
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See chapter 'Writing R documentation files' in the 'Writing R
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Extensions' manual.
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* checking for code/documentation mismatches ... WARNING
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Codoc mismatches from documentation object 'calibMuso':
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calibMuso
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Code: function(settings = setupMuso(), calibrationPar = NULL,
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parameters = NULL, outVars = NULL, timee = "d",
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debugging = FALSE, logfilename = NULL, keepEpc =
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FALSE, export = FALSE, silent = FALSE, aggressive =
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FALSE, keepBinary = FALSE, binaryPlace = "./",
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fileToChange = "epc", skipSpinup = TRUE,
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modifyOriginal = FALSE, prettyOut = FALSE,
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postProcString = NULL, doBackup = TRUE)
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Docs: function(settings, parameters = NULL, timee = "d", debugging =
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FALSE, logfilename = NULL, keepEpc = FALSE, export =
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FALSE, silent = FALSE, aggressive = FALSE, leapYear =
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FALSE)
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Argument names in code not in docs:
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calibrationPar outVars keepBinary binaryPlace fileToChange
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skipSpinup modifyOriginal prettyOut postProcString doBackup
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Argument names in docs not in code:
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leapYear
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Mismatches in argument names (first 3):
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Position: 2 Code: calibrationPar Docs: parameters
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Position: 3 Code: parameters Docs: timee
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Position: 4 Code: outVars Docs: debugging
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Mismatches in argument default values:
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Name: 'settings' Code: setupMuso() Docs:
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Codoc mismatches from documentation object 'calibrateMuso':
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calibrateMuso
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Code: function(measuredData, parameters = read.csv("parameters.csv",
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stringsAsFactor = FALSE), startDate = NULL, endDate =
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NULL, formatString = "%Y-%m-%d", dataVar, outLoc =
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"./calib", preTag = "cal-", settings = setupMuso(),
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outVars = NULL, iterations = 100, skipSpinup = TRUE,
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plotName = "calib.jpg", modifyOriginal = TRUE,
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likelihood, uncertainity = NULL, naVal = NULL,
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postProcString = NULL, thread_prefix = "thread",
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numCores = max(c(parallel::detectCores() - 1, 1)), pb
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= txtProgressBar(min = 0, max = iterations, style =
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3), maxLikelihoodEpc = TRUE, pbUpdate =
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setTxtProgressBar, outputLoc = "./", method = "GLUE",
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lg = FALSE, w = NULL, ...)
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Docs: function(measuredData, parameters = read.csv("parameters.csv",
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stringsAsFactor = FALSE), startDate = NULL, endDate =
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NULL, formatString = "%Y-%m-%d", dataVar, outLoc =
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"./calib", preTag = "cal-", settings = setupMuso(),
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outVars = NULL, iterations = 100, skipSpinup = TRUE,
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plotName = "calib.jpg", modifyOriginal = TRUE,
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likelihood, uncertainity = NULL, naVal = NULL,
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postProcString = NULL, thread_prefix = "thread",
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numCores = (parallel::detectCores() - 1), pb =
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txtProgressBar(min = 0, max = iterations, style = 3),
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maxLikelihoodEpc = TRUE, pbUpdate = setTxtProgressBar,
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outputLoc = "./", method = "GLUE", lg = FALSE, w =
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NULL, ...)
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Mismatches in argument default values:
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Name: 'numCores' Code: max(c(parallel::detectCores() - 1, 1)) Docs: (parallel::detectCores() - 1)
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Codoc mismatches from documentation object 'musoMapping':
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musoMapping
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Code: function(code, mapData =
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getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]])
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Docs: function(code, mapData = NULL)
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Mismatches in argument default values:
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Name: 'mapData' Code: getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]] Docs: NULL
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Codoc mismatches from documentation object 'musoMappingFind':
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musoMapping
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Code: function(code, mapData =
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getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]])
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Docs: function(code, mapData = NULL)
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Mismatches in argument default values:
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Name: 'mapData' Code: getOption("RMuso_varTable")[[as.character(getOption("RMuso_version"))]] Docs: NULL
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Codoc mismatches from documentation object 'normalMuso':
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normalMuso
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Code: function(settings = NULL, parameters = NULL, timee = "d",
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debugging = FALSE, logfilename = NULL, keepEpc =
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FALSE, export = FALSE, silent = FALSE, aggressive =
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FALSE, leapYear = FALSE, binaryPlace = NULL,
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fileToChange = "epc", keepBinary = FALSE)
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Docs: function(settings, parameters = NULL, timee = "d", debugging =
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FALSE, logfilename = NULL, keepEpc = FALSE, export =
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FALSE, silent = FALSE, aggressive = FALSE, leapYear =
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FALSE)
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Argument names in code not in docs:
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binaryPlace fileToChange keepBinary
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Mismatches in argument default values:
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Name: 'settings' Code: NULL Docs:
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Codoc mismatches from documentation object 'plotMuso':
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plotMuso
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Code: function(settings = NULL, variable = "all", timee = "d", silent
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= TRUE, calibrationPar = NULL, parameters = NULL,
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debugging = FALSE, keepEpc = FALSE, fileToChange =
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"epc", logfilename = NULL, aggressive = FALSE,
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leapYear = FALSE, plotName = NULL, plotType = "cts",
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layerPlot = FALSE, colour = "blue", skipSpinup = TRUE,
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fromData = FALSE, timeFrame = "day", selectYear =
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NULL, groupFun = mean, separateFile = FALSE, dpi =
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300, postProcString = NULL)
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Docs: function(settings, variable, timee = "d", silent = TRUE,
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debugging = FALSE, keepEpc = FALSE, logfilename =
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NULL, aggressive = FALSE, leapYear = FALSE, export =
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FALSE)
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Argument names in code not in docs:
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calibrationPar parameters fileToChange plotName plotType layerPlot
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colour skipSpinup fromData timeFrame selectYear groupFun
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separateFile dpi postProcString
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Argument names in docs not in code:
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export
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Mismatches in argument names (first 3):
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Position: 5 Code: calibrationPar Docs: debugging
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Position: 6 Code: parameters Docs: keepEpc
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Position: 7 Code: debugging Docs: logfilename
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Mismatches in argument default values:
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Name: 'settings' Code: NULL Docs:
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Name: 'variable' Code: "all" Docs:
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|
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Codoc mismatches from documentation object 'plotMusoWithData':
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plotMuso
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Code: function(settings = NULL, variable = "all", timee = "d", silent
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= TRUE, calibrationPar = NULL, parameters = NULL,
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debugging = FALSE, keepEpc = FALSE, fileToChange =
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"epc", logfilename = NULL, aggressive = FALSE,
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|
leapYear = FALSE, plotName = NULL, plotType = "cts",
|
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layerPlot = FALSE, colour = "blue", skipSpinup = TRUE,
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|
fromData = FALSE, timeFrame = "day", selectYear =
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|
NULL, groupFun = mean, separateFile = FALSE, dpi =
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300, postProcString = NULL)
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|
Docs: function(settings, variable, timee = "d", silent = TRUE,
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|
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
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|
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:
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|
Name: 'variable' Code: "all" Docs:
|
|
|
|
Codoc mismatches from documentation object 'runMuso':
|
|
calibMuso
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|
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
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|
= NULL, metInput = NULL, CO2Input = NULL, plantInput =
|
|
NULL, thinInput = NULL, mowInput = NULL, grazInput =
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|
NULL, harvInput = NULL, plougInput = NULL, fertInput =
|
|
NULL, irrInput = NULL, nitInput = NULL, iniInput =
|
|
NULL, epcInput = NULL, mapData = NULL, leapYear =
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|
FALSE, version = 6, doCopy = TRUE)
|
|
Docs: function(executable = NULL, parallel = F, calibrationPar =
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|
c(1), outputLoc = NULL, inputLoc = NULL, metInput =
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|
NULL, CO2Input = NULL, plantInput = NULL, thinInput =
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|
NULL, mowInput = NULL, grazInput = NULL, harvInput =
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|
NULL, plougInput = NULL, fertInput = NULL, irrInput =
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|
NULL, nitInput = NULL, iniInput = NULL, epcInput =
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NULL)
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Argument names in code not in docs:
|
|
modelOutputs mapData leapYear version doCopy
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|
Mismatches in argument names (first 3):
|
|
Position: 5 Code: modelOutputs Docs: inputLoc
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|
Position: 6 Code: inputLoc Docs: metInput
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|
Position: 7 Code: metInput Docs: CO2Input
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|
|
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
|