* using log directory 'd:/Rcompile/CRANpkg/local/3.3/MethComp.Rcheck' * using R version 3.3.2 (2016-10-31) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'MethComp/DESCRIPTION' ... OK * this is package 'MethComp' version '1.22.2' * 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 'MethComp' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to 'nlme' which was already attached by Depends. Please remove these calls from your code. 'library' or 'require' calls in package code: 'BRugs' 'R2WinBUGS' 'coda' 'rjags' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: 'nlme' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': 'nlme:::VarCorr' See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: 'VC.est.fixed' 'VC.est.random' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE AB.plot: no visible global function definition for 'complete.cases' AB.plot: no visible global function definition for 'ave' AB.plot: no visible global function definition for 'segments' AltReg: no visible global function definition for 'complete.cases' AltReg: no visible global function definition for 'fitted' AltReg: no visible global function definition for 'lm' AltReg: no visible global function definition for 'lme' AltReg: no visible global function definition for 'flush.console' BA.est: no visible global function definition for 'lmeControl' BA.est: no visible global function definition for 'qt' BA.plot: no visible global function definition for 'grey' BA.plot: no visible global function definition for 'str' BlandAltman: no visible global function definition for 'qt' BlandAltman: no visible global function definition for 'sd' BlandAltman: no visible global function definition for 'pt' BlandAltman : cnr: no visible global function definition for 'par' BlandAltman: no visible global function definition for 'lm' BlandAltman: no visible global function definition for 'coef' BlandAltman: no visible global function definition for 'plot.default' BlandAltman: no visible global function definition for 'abline' BlandAltman: no visible global function definition for 'text' BlandAltman: no visible global function definition for 'points' BlandAltman: no visible global function definition for 'axis' BlandAltman: no visible global function definition for 'box' BlandAltman: no visible global function definition for 'par' Deming: no visible global function definition for 'complete.cases' Deming: no visible global function definition for 'var' Deming: no visible global function definition for 'cov' Deming: no visible binding for global variable 'quantile' MCmcmc: no visible global function definition for 'flush.console' MCmcmc: no visible global function definition for 'jags.model' MCmcmc: no visible global function definition for 'bugs' MCmcmc: no visible global function definition for 'read.bugs' Meth.sim: no visible global function definition for 'runif' Meth.sim: no visible global function definition for 'rnorm' Meth.sim: no visible global function definition for 'rbinom' PBreg: no visible global function definition for 'complete.cases' PBreg: no visible global function definition for 'combn' PBreg: no visible global function definition for 'qnorm' PBreg: no visible global function definition for 'median' TDI: no visible global function definition for 'sd' TDI: no visible global function definition for 'qnorm' TDI : FF: no visible global function definition for 'pnorm' TDI: no visible global function definition for 'uniroot' TDI: no visible global function definition for 'quantile' VC.est: no visible global function definition for 'lmeControl' VC.est.fixed: no visible global function definition for 'lmeControl' VC.est.fixed: no visible global function definition for 'lme' VC.est.fixed: no visible global function definition for 'pdIdent' VC.est.fixed: no visible global function definition for 'varIdent' VC.est.fixed: no visible global function definition for 'pdDiag' VC.est.fixed: no visible global function definition for 'pdSymm' VC.est.fixed: no visible global function definition for 'residuals' VC.est.random: no visible global function definition for 'lmeControl' VC.est.random: no visible global function definition for 'lme' VC.est.random: no visible global function definition for 'pdBlocked' VC.est.random: no visible global function definition for 'pdIdent' VC.est.random: no visible global function definition for 'varIdent' VC.est.random: no visible global function definition for 'ranef' VC.est.random: no visible global function definition for 'pdDiag' VC.est.random: no visible global function definition for 'tail' VC.est.random: no visible global function definition for 'residuals' bothlines: no visible global function definition for 'abline' bothlines: no visible global function definition for 'lm' bothlines: no visible global function definition for 'coef' connect2mean: no visible global function definition for 'ave' connect2mean: no visible global function definition for 'segments' corr.measures: no visible global function definition for 'complete.cases' corr.measures: no visible global function definition for 'var' corr.measures: no visible global function definition for 'cov' corr.measures: no visible global function definition for 'cor' do.DA.reg: no visible global function definition for 'complete.cases' do.DA.reg: no visible global function definition for 'lm' find.mean: no visible global function definition for 'varnames' find.vars: no visible global function definition for 'varnames' lines.MethComp: no visible global function definition for 'par' lines.MethComp: no visible global function definition for 'qt' lines.MethComp: no visible global function definition for 'matlines' lines.MethComp: no visible global function definition for 'axis' lines.MethComp: no visible global function definition for 'box' mean.Meth: no visible global function definition for 'aggregate' middle: no visible global function definition for 'quantile' pairs.MCmcmc: no visible global function definition for 'rainbow' pairs.MCmcmc: no visible global function definition for 'pairs' pairs.MCmcmc: no visible global function definition for 'varnames' perm.repl: no visible global function definition for 'runif' plot.MCmcmc: no visible global function definition for 'gray' plot.MCmcmc : conv.pair: no visible global function definition for 'abline' plot.MCmcmc : conv.pair: no visible global function definition for 'strwidth' plot.MCmcmc : conv.pair: no visible global function definition for 'strheight' plot.MCmcmc : conv.pair: no visible global function definition for 'rect' plot.MCmcmc : conv.pair: no visible global function definition for 'par' plot.MCmcmc : conv.pair: no visible global function definition for 'text' plot.MCmcmc : conv.pair: no visible global function definition for 'box' plot.MCmcmc: no visible global function definition for 'par' plot.MCmcmc: no visible global function definition for 'plot' plot.MCmcmc: no visible global function definition for 'axis' plot.MCmcmc: no visible global function definition for 'mtext' plot.Meth : pnl: no visible global function definition for 'abline' plot.Meth : pnl: no visible global function definition for 'points' plot.Meth : pnu: no visible global function definition for 'sd' plot.Meth : pnu: no visible global function definition for 'abline' plot.Meth : pnu: no visible global function definition for 'points' plot.Meth: no visible global function definition for 'par' plot.Meth: no visible global function definition for 'plot' plot.Meth: no visible global function definition for 'text' plot.Meth: no visible global function definition for 'box' plot.Meth: no visible global function definition for 'axis' plot.MethComp: no visible global function definition for 'grey' plot.MethComp: no visible global function definition for 'plot' plot.MethComp: no visible global function definition for 'abline' plot.MethComp: no visible global function definition for 'box' plot.MethComp: no visible global function definition for 'strwidth' plot.MethComp: no visible global function definition for 'strheight' plot.MethComp: no visible global function definition for 'par' plot.MethComp: no visible global function definition for 'rect' plot.MethComp: no visible global function definition for 'text' plot.PBreg: no visible global function definition for 'predict' plot.PBreg: no visible global function definition for 'plot' plot.PBreg: no visible global function definition for 'polygon' plot.PBreg: no visible global function definition for 'abline' plot.PBreg: no visible global function definition for 'points' plot.PBreg: no visible global function definition for 'text' plot.PBreg: no visible global function definition for 'IQR' plot.PBreg: no visible global function definition for 'hist' plot.PBreg: no visible global function definition for 'density' plot.PBreg: no visible global function definition for 'lines' plot.VarComp: no visible global function definition for 'gray' plot.VarComp: no visible global function definition for 'density' plot.VarComp: no visible global function definition for 'quantile' plot.VarComp: no visible global function definition for 'plot' plot.VarComp: no visible global function definition for 'abline' plot.VarComp: no visible global function definition for 'lines' plot.VarComp: no visible global function definition for 'axis' plot.VarComp: no visible global function definition for 'par' plot.VarComp: no visible global function definition for 'text' plot.VarComp: no visible global function definition for 'mtext' points.MethComp: no visible global function definition for 'points' post.MCmcmc: no visible global function definition for 'rainbow' post.mean: no visible global function definition for 'gray' post.sd: no visible global function definition for 'gray' predict.PBreg: no visible global function definition for 'qnorm' predict.PBreg: no visible global function definition for 'median' predict.PBreg: no visible global function definition for 'quantile' print.MCmcmc: no visible global function definition for 'ftable' print.MethComp: no visible global function definition for 'ftable' sort.Meth: no visible global function definition for 'ave' subset.MCmcmc : char.2.num: no visible global function definition for 'varnames' summary.MCmcmc: no visible binding for global variable 'quantile' summary.Meth: no visible global function definition for 'addmargins' to.long: no visible global function definition for 'reshape' to.wide: no visible global function definition for 'reshape' trace.mean: no visible global function definition for 'gray' trace.sd: no visible global function definition for 'gray' Undefined global functions or variables: IQR abline addmargins aggregate ave axis box bugs coef combn complete.cases cor cov density fitted flush.console ftable gray grey hist jags.model lines lm lme lmeControl matlines median mtext pairs par pdBlocked pdDiag pdIdent pdSymm plot plot.default pnorm points polygon predict pt qnorm qt quantile rainbow ranef rbinom read.bugs rect reshape residuals rnorm runif sd segments str strheight strwidth tail text uniroot var varIdent varnames Consider adding importFrom("grDevices", "gray", "grey", "rainbow") importFrom("graphics", "abline", "axis", "box", "hist", "lines", "matlines", "mtext", "pairs", "par", "plot", "plot.default", "points", "polygon", "rect", "segments", "strheight", "strwidth", "text") importFrom("stats", "IQR", "addmargins", "aggregate", "ave", "coef", "complete.cases", "cor", "cov", "density", "fitted", "ftable", "lm", "median", "pnorm", "predict", "pt", "qnorm", "qt", "quantile", "rbinom", "reshape", "residuals", "rnorm", "runif", "sd", "uniroot", "var") importFrom("utils", "combn", "flush.console", "str", "tail") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * 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 sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [31s] OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs