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datacloning / dclone

Data Cloning and MCMC Tools for Maximum Likelihood Methods
https://github.com/datacloning/dclone
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Fix CRAN notes: namespace issues #3

Closed psolymos closed 8 years ago

psolymos commented 8 years ago

using R Under development (unstable) (2016-01-10 r69905) using platform: x86_64-pc-linux-gnu (64-bit) using session charset: UTF-8 checking for file ‘dclone/DESCRIPTION’ ... OK checking extension type ... Package this is package ‘dclone’ version ‘2.0-0’ checking package namespace information ... OK checking package dependencies ... OK checking if this is a source package ... OK checking if there is a namespace ... OK checking for executable files ... OK checking for hidden files and directories ... OK checking for portable file names ... OK checking for sufficient/correct file permissions ... OK checking whether package ‘dclone’ 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' calls in package code: ‘BRugs’ ‘MASS’ ‘R2OpenBUGS’ ‘R2WinBUGS’ ‘snow’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘parallel’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. checking S3 generic/method consistency ... OK checking replacement functions ... OK checking foreign function calls ... OK checking R code for possible problems ... NOTE .dcFit: no visible global function definition for ‘flush.console’ .dcFit: no visible global function definition for ‘varnames’ .dcFit: no visible global function definition for ‘nchain’ [.mcmc.list.dc: no visible global function definition for ‘as’ as.mcmc.list.bugs : : no visible global function definition for ‘mcmc’ bugs.parfit: no visible global function definition for ‘flush.console’ bugs.parfit: no visible binding for global variable ‘as.mcmc’ chisq.diag.mcmc.list: no visible global function definition for ‘var’ chisq.diag.mcmc.list: no visible global function definition for ‘qchisq’ chisq.diag.mcmc.list: no visible global function definition for ‘cor’ clusterSplitSB: no visible global function definition for ‘clusterSplit’ codaSamples: no visible global function definition for ‘coda.samples’ confint.mcmc.list.dc: no visible global function definition for ‘varnames’ confint.mcmc.list.dc: no visible global function definition for ‘qnorm’ dc.parfit: no visible global function definition for ‘flush.console’ dc.parfit : dcparallel: no visible global function definition for ‘varnames’ dc.parfit: no visible global function definition for ‘varnames’ dc.parfit: no visible global function definition for ‘list.modules’ dc.parfit : assemblyfun: no visible binding for global variable ‘as.mcmc’ dc.parfit: no visible global function definition for ‘nchain’ dcdiag.default: no visible binding for global variable ‘varnames’ dcsd.mcmc.list: no visible binding for global variable ‘sd’ errlines.default: no visible global function definition for ‘polygon’ errlines.default: no visible global function definition for ‘lines’ extractdcdiag.default: no visible global function definition for ‘nchain’ extractdcdiag.default: no visible global function definition for ‘nvar’ extractdcdiag.default: no visible global function definition for ‘gelman.diag’ extractdctable.default: no visible binding for global variable ‘sd’ extractdctable.default: no visible global function definition for ‘nchain’ extractdctable.default: no visible global function definition for ‘gelman.diag’ extractdctable.default: no visible global function definition for ‘varnames’ jags.parfit: no visible global function definition for ‘clusterEvalQ’ jags.parfit: no visible global function definition for ‘list.modules’ jags.parfit: no visible global function definition for ‘flush.console’ jags.parfit: no visible binding for global variable ‘as.mcmc’ lambdamax.diag.mcmc.list: no visible global function definition for ‘var’ lambdamax.diag.mcmc.list: no visible global function definition for ‘nvar’ mclapplySB: no visible global function definition for ‘mclapply’ pairs.mcmc.list: no visible global function definition for ‘terrain.colors’ pairs.mcmc.list: no visible global function definition for ‘niter’ pairs.mcmc.list : fun.lower0: no visible global function definition for ‘kde2d’ pairs.mcmc.list : fun.lower0: no visible global function definition for ‘image’ pairs.mcmc.list : fun.lower0: no visible global function definition for ‘abline’ pairs.mcmc.list : fun.upper: no visible global function definition for ‘abline’ pairs.mcmc.list : fun.upper: no visible global function definition for ‘points’ pairs.mcmc.list : panel.hist.density: no visible global function definition for ‘par’ pairs.mcmc.list : panel.hist.density: no visible global function definition for ‘hist’ pairs.mcmc.list : panel.hist.density: no visible global function definition for ‘rect’ pairs.mcmc.list : panel.hist.density: no visible global function definition for ‘lines’ pairs.mcmc.list : panel.hist.density: no visible global function definition for ‘rug’ pairs.mcmc.list: no visible global function definition for ‘pairs.default’ pairs.mcmc.list: no visible global function definition for ‘varnames’ parCodaSamples: no visible binding for global variable ‘as.mcmc’ parDosa: no visible global function definition for ‘clusterEvalQ’ parDosa: no visible global function definition for ‘clusterSetupRNG’ parDosa: no visible global function definition for ‘parLapply’ parDosa: no visible global function definition for ‘clusterExport’ parDosa: no visible global function definition for ‘clusterApplyLB’ parJagsModel: no visible global function definition for ‘clusterEvalQ’ parJagsModel: no visible global function definition for ‘list.modules’ parLapplySB: no visible global function definition for ‘clusterApply’ parLapplySB: no visible global function definition for ‘docall’ parLapplySLB: no visible global function definition for ‘clusterApplyLB’ parListFactories: no visible global function definition for ‘clusterEvalQ’ parListFactories: no visible global function definition for ‘clusterCall’ parListModules: no visible global function definition for ‘clusterEvalQ’ parLoadModule: no visible global function definition for ‘clusterEvalQ’ parLoadModule: no visible global function definition for ‘parLapply’ parSetFactory: no visible global function definition for ‘clusterEvalQ’ parSetFactory: no visible global function definition for ‘clusterCall’ parUnloadModule: no visible global function definition for ‘clusterEvalQ’ parUnloadModule: no visible global function definition for ‘clusterCall’ parUpdate: no visible global function definition for ‘clusterEvalQ’ plot.chisq.diag: no visible global function definition for ‘qqplot’ plot.chisq.diag: no visible global function definition for ‘abline’ plot.dcdiag : plotit: no visible global function definition for ‘plot’ plot.dcdiag : plotit: no visible global function definition for ‘axis’ plot.dcdiag : plotit: no visible global function definition for ‘box’ plot.dcdiag : plotit: no visible global function definition for ‘legend’ plot.dcdiag : plotit: no visible global function definition for ‘lines’ plot.dcdiag: no visible global function definition for ‘par’ plot.dctable : plotit: no visible global function definition for ‘plot’ plot.dctable : plotit: no visible global function definition for ‘points’ plot.dctable : plotit: no visible global function definition for ‘axis’ plot.dctable : plotit: no visible global function definition for ‘box’ plot.dctable : plotit: no visible global function definition for ‘legend’ plot.dctable : plotit: no visible global function definition for ‘lines’ plot.dctable: no visible global function definition for ‘par’ plotClusterSize: no visible global function definition for ‘clusterSplit’ plotClusterSize: no visible global function definition for ‘plot.new’ plotClusterSize: no visible global function definition for ‘plot.window’ plotClusterSize: no visible global function definition for ‘box’ plotClusterSize: no visible global function definition for ‘axis’ plotClusterSize: no visible global function definition for ‘title’ plotClusterSize: no visible global function definition for ‘polygon’ plotClusterSize: no visible global function definition for ‘text’ snowWrapper: no visible global function definition for ‘clusterEvalQ’ snowWrapper: no visible global function definition for ‘clusterSetupRNG’ snowWrapper: no visible global function definition for ‘parLapply’ snowWrapper: no visible global function definition for ‘clusterExport’ snowWrapper: no visible global function definition for ‘clusterApplyLB’ stack.mcmc.list: no visible global function definition for ‘varnames’ stack.mcmc.list: no visible global function definition for ‘nvar’ stack.mcmc.list: no visible global function definition for ‘time’ stack.mcmc.list: no visible global function definition for ‘nchain’ stack.mcmc.list: no visible global function definition for ‘niter’ summary.mcmc.list.dc: no visible global function definition for ‘nchain’ summary.mcmc.list.dc: no visible global function definition for ‘gelman.diag’ summary.mcmc.list.dc: no visible global function definition for ‘nvar’ summary.mcmc.list.dc: no visible global function definition for ‘varnames’ update.mcmc.list: no visible global function definition for ‘varnames’ update.mcmc.list: no visible global function definition for ‘niter’ update.mcmc.list: no visible global function definition for ‘coda.samples’ vcov.mcmc.list: no visible global function definition for ‘cov’ vcov.mcmc.list.dc: no visible global function definition for ‘cov’ Undefined global functions or variables: abline as as.mcmc axis box clusterApply clusterApplyLB clusterCall clusterEvalQ clusterExport clusterSetupRNG clusterSplit coda.samples cor cov docall flush.console gelman.diag hist image kde2d legend lines list.modules mclapply mcmc nchain niter nvar pairs.default par parLapply plot plot.new plot.window points polygon qchisq qnorm qqplot rect rug sd terrain.colors text time title var varnames Consider adding importFrom("grDevices", "terrain.colors") importFrom("graphics", "abline", "axis", "box", "hist", "image", "legend", "lines", "pairs.default", "par", "plot", "plot.new", "plot.window", "points", "polygon", "rect", "rug", "text", "title") importFrom("methods", "as") importFrom("stats", "cor", "cov", "qchisq", "qnorm", "qqplot", "sd", "time", "var") importFrom("utils", "flush.console") to your NAMESPACE (and ensure that your DESCRIPTION Imports field contains 'methods'). checking Rd files ... OK checking Rd metadata ... OK checking Rd line widths ... 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 examples ... [3s/3s] OK checking PDF version of manual ... OK DONE Status: 2 NOTEs