* using log directory 'd:/Rcompile/CRANpkg/local/3.3/FAiR.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 'FAiR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'FAiR' version '0.4-15' * package encoding: UTF-8 * 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 'FAiR' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking 'build' 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 * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK ** checking use of S3 registration ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK ** checking loading without being on the library search path ... OK ** checking use of S3 registration ... OK * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: 'Rgraphviz' 'corpcor' 'energy' 'mvnmle' 'mvnormtest' 'nFactors' 'polycor' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Calls with DUP: .C(FAiR_QD_sum, sum = numeric(1), x = x, middle = middle, length = length(x), DUP = FALSE, NAOK = TRUE) .C(FAiR_QD_grad, grad = numeric(length_x), x = x, middle = middle, length = length_x, holder = numeric(length_x), DUP = FALSE, NAOK = TRUE) .C("exhaustive_mve", number = as.integer(0), combos = combos, lengthcombos = length(combos), Xdata = as.double(X), Xrow = nrow(X), Xcol = ncol(X), DUP = FALSE, PACKAGE = "FAiR") DUP is no longer supported and will be ignored. * checking R code for possible problems ... NOTE .onAttach: no visible global function definition for 'packageDescription' .onAttach: no visible global function definition for 'flush.console' FA2draws: no visible global function definition for 'runif' FAiR_ADF: no visible global function definition for 'Matrix' FAiR_ADF_robust: no visible global function definition for 'CovMcd' FAiR_ADF_unbiased: no visible global function definition for 'CovMcd' FAiR_ADF_unbiased: no visible global function definition for 'cov.wt' FAiR_ADF_unbiased: no visible global function definition for 'huberM' FAiR_DAG: no visible global function definition for 'nodes' FAiR_DAG: no visible global function definition for 'addEdge' FAiR_DAG: no visible global function definition for 'subGraph' FAiR_HK: no visible global function definition for 'median' FAiR_Mcd: no visible global function definition for 'CovMcd' FAiR_Mcd: no visible global function definition for 'cov2cor' FAiR_PACE : temp.fun: no visible global function definition for 'complete.cases' FAiR_PACE: no visible global function definition for 'combn' FAiR_RMSEA : foo: no visible global function definition for 'pchisq' FAiR_RMSEA: no visible global function definition for 'uniroot' FAiR_RMSEA: no visible global function definition for 'pchisq' FAiR_Steiger : foo: no visible global function definition for 'pchisq' FAiR_Steiger: no visible global function definition for 'uniroot' FAiR_blockanator: no visible global function definition for 'gmessage' FAiR_bootstrap2dppMatrix: no visible global function definition for 'Matrix' FAiR_bounds_coef: no visible global function definition for 'gmessage' FAiR_bounds_cormat: no visible global function definition for 'gmessage' FAiR_constraints_1st : FAiR_criterion_evRF_1st: no visible global function definition for 'cov2cor' FAiR_constraints_1st : FAiR_criterion_dist_cols_1st: no visible global function definition for 'dist' FAiR_constraints_2nd : FAiR_criterion_dist_cols_2nd: no visible global function definition for 'dist' FAiR_constraints_2nd : FAiR_criterion_evRF_2nd: no visible global function definition for 'cov2cor' FAiR_cor.rank: no visible global function definition for 'cor' FAiR_cor.rank: no visible global function definition for 'Diagonal' FAiR_cov.shrink: no visible global function definition for 'cov.shrink' FAiR_cov.shrink: no visible global function definition for 'Diagonal' FAiR_cov.shrink: no visible binding for global variable 'weighted.mean' FAiR_cov.shrink: no visible global function definition for 'cov2cor' FAiR_deriv_matrix: no visible global function definition for 'numericDeriv' FAiR_draws2CI: no visible binding for global variable 'quantile' FAiR_edit: no visible global function definition for 'ggroup' FAiR_edit: no visible global function definition for 'glabel' FAiR_edit: no visible global function definition for 'flush.console' FAiR_edit: no visible global function definition for 'gdf' FAiR_edit: no visible global function definition for 'gbasicdialog' FAiR_edit: no visible global function definition for 'guiToolkit' FAiR_equality_restrictions: no visible global function definition for 'gmessage' FAiR_get_answer: no visible global function definition for 'ggroup' FAiR_get_answer: no visible global function definition for 'glabel' FAiR_get_answer: no visible global function definition for 'gseparator' FAiR_get_answer: no visible global function definition for 'gradio' FAiR_get_answer: no visible global function definition for 'gslider' FAiR_get_answer: no visible global function definition for 'gcheckboxgroup' FAiR_get_answer: no visible global function definition for 'flush.console' FAiR_get_answer: no visible global function definition for 'gbasicdialog' FAiR_get_answer: no visible global function definition for 'guiToolkit' FAiR_get_mapping_rule_args: no visible global function definition for 'gmessage' FAiR_hetcor: no visible global function definition for 'hetcor' FAiR_hetcor: no visible global function definition for 'cor' FAiR_hetcor: no visible global function definition for 'Diagonal' FAiR_indicators_FC: no visible global function definition for 'gmessage' FAiR_make_manifest.data_numeric: no visible global function definition for 'cov.wt' FAiR_make_manifest.data_numeric: no visible binding for global variable 'weighted.mean' FAiR_make_manifest.data_numeric: no visible global function definition for 'cov2cor' FAiR_make_manifest_list: no visible global function definition for 'Diagonal' FAiR_make_manifest_list: no visible global function definition for 'cov2cor' FAiR_make_starts_for_Rotate: no visible global function definition for 'combn' FAiR_make_target: no visible global function definition for 'gmessage' FAiR_mlest: no visible global function definition for 'mlest' FAiR_mlest: no visible global function definition for 'cov2cor' FAiR_nearPD: no visible global function definition for 'cov2cor' FAiR_numeric_gradient: no visible global function definition for 'numericDeriv' FAiR_order_FC: no visible global function definition for 'gmessage' FAiR_paired: no visible global function definition for 'pchisq' FAiR_parallel_4th: no visible global function definition for 'rnorm' FAiR_parallel_4th: no visible global function definition for 'cov.wt' FAiR_parallel_4th: no visible global function definition for 'cov2cor' FAiR_parallel_4th : SEcentile: no visible global function definition for 'dnorm' FAiR_parallel_4th : SEcentile: no visible global function definition for 'qnorm' FAiR_parallel_4th: no visible binding for global variable 'sd' FAiR_parallel_4th : quant: no visible global function definition for 'quantile' FAiR_parse_formula: no visible global function definition for 'terms' FAiR_peg_coefficients: no visible global function definition for 'gmessage' FAiR_profile: no visible global function definition for 'par' FAiR_profile: no visible global function definition for 'abline' FAiR_quick_Rotate: no visible global function definition for 'targetT' FAiR_quick_Rotate: no visible global function definition for 'GPForth' FAiR_quick_Rotate: no visible global function definition for 'targetQ' FAiR_quick_Rotate: no visible global function definition for 'GPFoblq' FAiR_quick_Rotate: no visible global function definition for 'optim' FAiR_show_manifest: no visible global function definition for 'pchisq' FAiR_show_manifest: no visible global function definition for 'cov2cor' FAiR_shrink: no visible global function definition for 'cov2cor' FAiR_stress_test: no visible global function definition for 'dev.off' FAiR_stress_test: no visible global function definition for 'BIC' FAiR_test_Browne84: no visible global function definition for 'pchisq' FAiR_test_SB94: no visible global function definition for 'pchisq' FAiR_test_T2: no visible global function definition for 'pf' FAiR_test_YB98: no visible global function definition for 'pchisq' FAiR_test_exact_fit: no visible global function definition for 'pchisq' FAiR_uniquify: no visible global function definition for 'runif' Factanal: no visible global function definition for 'factanal' Factanal: no visible global function definition for 'flush.console' Factanal: no visible global function definition for 'optim' Rotate: no visible global function definition for 'optim' write.CEFA: no visible global function definition for 'write.table' write.cefa: no visible global function definition for 'write.table' create_FAobject,restrictions.independent-manifest.basic: no visible binding for global variable 'factors' create_start,restrictions-manifest.basic : : no visible global function definition for 'runif' create_start,restrictions.1storder-manifest.basic : : no visible global function definition for 'runif' create_start,restrictions.1storder-manifest.basic: no visible global function definition for 'GPForth' create_start,restrictions.1storder-manifest.basic: no visible global function definition for 'runif' create_start,restrictions.1storder-manifest.basic: no visible global function definition for 'rnorm' create_start,restrictions.2ndorder-manifest.basic : : no visible global function definition for 'runif' create_start,restrictions.2ndorder-manifest.basic: no visible global function definition for 'GPForth' create_start,restrictions.2ndorder-manifest.basic: no visible global function definition for 'runif' create_start,restrictions.2ndorder-manifest.basic: no visible global function definition for 'rnorm' create_start,restrictions.factanal-manifest.basic : : no visible global function definition for 'runif' create_start,restrictions.general-manifest.basic : : no visible global function definition for 'runif' create_start,restrictions.general-manifest.basic: no visible global function definition for 'GPForth' create_start,restrictions.general-manifest.basic: no visible global function definition for 'runif' create_start,restrictions.general-manifest.basic: no visible global function definition for 'rnorm' create_start,restrictions.orthonormal-manifest.basic : beta_fun: no visible global function definition for 'runif' create_start,restrictions.orthonormal-manifest.basic: no visible global function definition for 'rnorm' make_manifest,formula-data.frame-missing: no visible global function definition for 'get_all_vars' make_manifest,formula-data.frame-missing: no visible binding for global variable 'Z' make_manifest,missing-missing-CovMcd: no visible global function definition for 'cov2cor' make_restrictions,manifest.basic-parameter.scale-missing-missing-missing-missing: no visible binding for global variable 'manfiest' make_restrictions,manifest.basic-parameter.scale-missing-missing-missing-missing: no visible binding for global variable 'criteria' pairs,FA: no visible global function definition for 'par' pairs,FA : : no visible global function definition for 'palette' pairs,FA : UP: no visible global function definition for 'abline' pairs,FA : UP: no visible global function definition for 'points' pairs,FA : LP: no visible global function definition for 'abline' pairs,FA : LP: no visible global function definition for 'segments' pairs,FA : TP: no visible global function definition for 'text' pairs,FA: no visible global function definition for 'pairs.default' plot,FA-missing: no visible global function definition for 'addEdge' plot,FA-missing: no visible binding for global variable 'toDot' plot,FA.2ndorder-missing: no visible global function definition for 'addEdge' plot,FA.2ndorder-missing: no visible global function definition for 'join' plot,FA.2ndorder-missing: no visible binding for global variable 'toDot' plot,FA.general-missing: no visible global function definition for 'join' plot,FA.general-missing: no visible binding for global variable 'toDot' plot,manifest.basic-missing: no visible global function definition for 'heatmap' plot,manifest.data.mcd-missing: no visible global function definition for 'heatmap' plot,summary.FA-ANY: no visible global function definition for 'heatmap' profile,FA.2ndorder: no visible global function definition for 'par' profile,FA.2ndorder: no visible global function definition for 'abline' profile,FA.general: no visible global function definition for 'par' profile,FA.general: no visible binding for global variable 'p' profile,FA.general: no visible global function definition for 'abline' restrictions2draws,restrictions.1storder-manifest.basic: no visible global function definition for 'rnorm' restrictions2draws,restrictions.1storder.EFA-manifest.basic: no visible global function definition for 'rnorm' restrictions2draws,restrictions.2ndorder-manifest.basic: no visible global function definition for 'rnorm' restrictions2draws,restrictions.general-manifest.basic: no visible global function definition for 'rnorm' restrictions2draws,restrictions.orthonormal-manifest.basic: no visible global function definition for 'rnorm' screeplot,FA: no visible global function definition for 'parallel' screeplot,FA: no visible global function definition for 'nScree' screeplot,FA: no visible global function definition for 'plotnScree' screeplot,manifest.basic: no visible global function definition for 'parallel' screeplot,manifest.basic: no visible global function definition for 'nScree' screeplot,manifest.basic: no visible global function definition for 'plotnScree' screeplot,manifest.data: no visible global function definition for 'parallel' screeplot,manifest.data: no visible global function definition for 'nScree' screeplot,manifest.data: no visible global function definition for 'plotnScree' screeplot,manifest.data: no visible global function definition for 'cov2cor' show,manifest.data: no visible global function definition for 'mshapiro.test' show,manifest.data: no visible global function definition for 'mvnorm.etest' show,restrictions: no visible global function definition for 'str' show,summary.FA: no visible binding for global variable 'sd' simulate,FA: no visible global function definition for 'runif' uniquenesses,restrictions: no visible binding for global variable 'restrictions' Undefined global functions or variables: BIC CovMcd Diagonal GPFoblq GPForth Matrix Z abline addEdge combn complete.cases cor cov.shrink cov.wt cov2cor criteria dev.off dist dnorm factanal factors flush.console gbasicdialog gcheckboxgroup gdf get_all_vars ggroup glabel gmessage gradio gseparator gslider guiToolkit heatmap hetcor huberM join manfiest median mlest mshapiro.test mvnorm.etest nScree nodes numericDeriv optim p packageDescription pairs.default palette par parallel pchisq pf plotnScree points qnorm quantile restrictions rnorm runif sd segments str subGraph targetQ targetT terms text toDot uniroot weighted.mean write.table Consider adding importFrom("grDevices", "dev.off", "palette") importFrom("graphics", "abline", "pairs.default", "par", "points", "segments", "text") importFrom("stats", "BIC", "complete.cases", "cor", "cov.wt", "cov2cor", "dist", "dnorm", "factanal", "get_all_vars", "heatmap", "median", "numericDeriv", "optim", "pchisq", "pf", "qnorm", "quantile", "rnorm", "runif", "sd", "terms", "uniroot", "weighted.mean") importFrom("utils", "combn", "flush.console", "packageDescription", "str", "write.table") 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... [13s] OK ** running examples for arch 'x64' ... [14s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... [23s] OK Running 'testsCFA.R' [0s] Running 'testsEFA.R' [0s] Running 'testsMANIFEST.R' [7s] Running 'testsMICRO.R' [11s] Running 'testsRESTRICTIONS.R' [4s] Running 'testsSEFA.R' [0s] ** running tests for arch 'x64' ... [24s] OK Running 'testsCFA.R' [0s] Running 'testsEFA.R' [0s] Running 'testsMANIFEST.R' [7s] Running 'testsMICRO.R' [11s] Running 'testsRESTRICTIONS.R' [5s] Running 'testsSEFA.R' [0s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking re-building of vignette outputs ... [9s] OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs