* using log directory 'd:/Rcompile/CRANpkg/local/3.3/GenABEL.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 'GenABEL/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'GenABEL' version '1.8-0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'GenABEL' can be installed ... OK * checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: doc 2.2Mb libs 2.3Mb * 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 * 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 ... NOTE Warning: no function found corresponding to methods exports from 'GenABEL' for: 'show' A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. ** 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 ... NOTE Warning: no function found corresponding to methods exports from 'GenABEL' for: 'show' A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. ** 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: 'DatABEL' 'genetics' 'haplo.stats' 'hglm' 'qvalue' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'GenABEL.data' 'MASS' 'methods' 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 GASurv: no visible global function definition for 'is' HWE.show: no visible global function definition for 'is' HWE.show: no visible global function definition for 'pchisq' LiLog: no visible global function definition for 'binomial' PGC: no visible global function definition for 'median' PGC: no visible global function definition for 'qchisq' PGC: no visible global function definition for 'ppoints' PGC: no visible global function definition for 'quantile' PGC : f2: no visible global function definition for 'ks.test' PGC : f2: no visible global function definition for 'median' PGC : f2: no visible global function definition for 'qchisq' PGC: no visible global function definition for 'abline' PGC: no visible global function definition for 'lines' VIFGC : Clust: no visible global function definition for 'as.dist' VIFGC : Clust: no visible global function definition for 'cmdscale' VIFGC : ClustN: no visible global function definition for 'kmeans' VIFGC : GC_VIF_nlm: no visible global function definition for 'ks.test' VIFGC : GC_VIF_nlm: no visible global function definition for 'qchisq' VIFGC : GC_VIF_nlm: no visible global function definition for 'median' VIFGC : GC_VIF: no visible global function definition for 'ks.test' VIFGC : GC_VIF: no visible global function definition for 'qchisq' VIFGC : GC_VIF: no visible global function definition for 'median' VIFGC: no visible global function definition for 'qchisq' VIFGC: no visible global function definition for 'median' VIFGC: no visible global function definition for 'ppoints' VIFGC: no visible global function definition for 'optimize' VIFGC: no visible global function definition for 'nlm' VIFGC: no visible global function definition for 'abline' VIFGC: no visible global function definition for 'lines' VIFGC_ovdom : Clust: no visible global function definition for 'as.dist' VIFGC_ovdom : Clust: no visible global function definition for 'cmdscale' VIFGC_ovdom : ClustN: no visible global function definition for 'kmeans' VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for 'ks.test' VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for 'qchisq' VIFGC_ovdom : GC_VIF_nlm: no visible global function definition for 'median' VIFGC_ovdom : GC_VIF: no visible global function definition for 'ks.test' VIFGC_ovdom : GC_VIF: no visible global function definition for 'qchisq' VIFGC_ovdom : GC_VIF: no visible global function definition for 'median' VIFGC_ovdom: no visible global function definition for 'qchisq' VIFGC_ovdom: no visible global function definition for 'ppoints' VIFGC_ovdom: no visible global function definition for 'optimize' VIFGC_ovdom: no visible global function definition for 'median' VIFGC_ovdom: no visible global function definition for 'nlm' VIFGC_ovdom: no visible global function definition for 'abline' Xcheck: no visible global function definition for 'is' Xfix: no visible global function definition for 'is' Xfix.internal: no visible global function definition for 'is' add.phdata: no visible global function definition for 'is' add.plot: no visible global function definition for 'is' add.plot: no visible global function definition for 'points' add.plot: no visible global function definition for 'image' arrange_probabel_phe: no visible global function definition for 'read.table' arrange_probabel_phe: no visible global function definition for 'databel' arrange_probabel_phe: no visible global function definition for 'write.table' as.character.gwaa.data: no visible global function definition for 'is' as.character.snp.data: no visible global function definition for 'is' as.double.gwaa.data: no visible global function definition for 'is' as.double.snp.data: no visible global function definition for 'is' as.genotype.gwaa.data: no visible global function definition for 'is' as.genotype.snp.data: no visible global function definition for 'is' as.genotype.snp.data: no visible global function definition for 'genotype' as.hsgeno.gwaa.data: no visible global function definition for 'is' as.hsgeno.snp.data: no visible global function definition for 'is' as.raw.snp.data: no visible global function definition for 'is' as.raw.snp.mx: no visible global function definition for 'is' autosomal: no visible global function definition for 'is' blurGenotype: no visible global function definition for 'is' catable: no visible global function definition for 'quantile' catable: no visible global function definition for 'is' ccfast: no visible global function definition for 'is' ccfast: no visible global function definition for 'flush.console' ccfast: no visible global function definition for 'pchisq' ccfast: no visible global function definition for 'new' ccfast.new: no visible global function definition for 'is' check.marker: no visible global function definition for 'is' check.marker.internal: no visible global function definition for 'is' check.marker.internal: no visible global function definition for 'flush.console' check.marker.internal: no visible global function definition for 'qvalue' check.marker.internal: no visible global function definition for 'sd' check.marker.internal: no visible global function definition for 'pchisq' check.trait: no visible global function definition for 'is' checkphengen: no visible global function definition for 'is' cocohet: no visible global function definition for 'is' cocohet: no visible global function definition for 'pchisq' convert.snp.affymetrix: no visible global function definition for 'is' convert.snp.mach: no visible global function definition for 'read.table' convert.snp.mach: no visible global function definition for 'new' descriptives.marker: no visible global function definition for 'is' descriptives.marker: no visible global function definition for 'sd' descriptives.marker: no visible global function definition for 'write.table' descriptives.scan: no visible global function definition for 'is' descriptives.scan: no visible global function definition for 'write.table' descriptives.trait: no visible global function definition for 'is' descriptives.trait: no visible global function definition for 'sd' descriptives.trait: no visible global function definition for 't.test' descriptives.trait: no visible global function definition for 'kruskal.test' descriptives.trait: no visible global function definition for 'fisher.test' descriptives.trait: no visible global function definition for 'write.table' dprfast: no visible global function definition for 'is' drop.out.points: no visible global function definition for 'var' dump.piece: no visible global function definition for 'write.table' egscore: no visible global function definition for 'is' egscore: no visible global function definition for 'as' egscore: no visible global function definition for 'model.frame' egscore: no visible binding for global variable 'na.omit' egscore: no visible global function definition for 'model.response' egscore: no visible global function definition for 'model.matrix' egscore: no visible global function definition for 'glm.fit' egscore: no visible global function definition for 'lm' egscore: no visible global function definition for 'flush.console' egscore: no visible global function definition for 'pchisq' egscore: no visible global function definition for 'new' egscore.old: no visible global function definition for 'is' egscore.old: no visible global function definition for 'as' egscore.old: no visible global function definition for 'model.frame' egscore.old: no visible binding for global variable 'na.omit' egscore.old: no visible global function definition for 'model.response' egscore.old: no visible global function definition for 'model.matrix' egscore.old: no visible global function definition for 'glm.fit' egscore.old: no visible global function definition for 'lm' egscore.old: no visible global function definition for 'flush.console' egscore.old: no visible global function definition for 'pchisq' estLambdaKS: no visible global function definition for 'optimize' estlambda: no visible global function definition for 'qchisq' estlambda: no visible global function definition for 'ppoints' estlambda: no visible global function definition for 'lm' estlambda: no visible global function definition for 'median' estlambda: no visible global function definition for 'par' estlambda: no visible global function definition for 'abline' export.impute: no visible global function definition for 'is' export.impute: no visible global function definition for 'write.table' export.merlin: no visible global function definition for 'is' export.merlin: no visible global function definition for 'new' export.merlin: no visible global function definition for 'write.table' export.plink: no visible global function definition for 'write.table' extract.annotation.impute: no visible global function definition for 'extract_text_file_columns' extract.annotation.mach: no visible global function definition for 'extract_text_file_columns' fcc: no visible global function definition for 'is' fcc.new: no visible global function definition for 'is' findRelatives: no visible global function definition for 'is' findRelatives: no visible global function definition for 'txtProgressBar' findRelatives: no visible global function definition for 'setTxtProgressBar' formetascore: no visible global function definition for 'is' formetascore: no visible global function definition for 'as' formetascore: no visible global function definition for 'model.frame' formetascore: no visible binding for global variable 'na.omit' generateOffspring : genSOG: no visible global function definition for 'runif' generateOffspring : infer: no visible global function definition for 'rbinom' generateOffspring: no visible global function definition for 'rbinom' get.snp.distr.plot: no visible global function definition for 'na.omit' get.snp.distr.plot: no visible global function definition for 'bitmap' get.snp.distr.plot: no visible global function definition for 'par' get.snp.distr.plot: no visible global function definition for 'bartlett.test' get.snp.distr.plot: no visible global function definition for 'boxplot' get.snp.distr.plot: no visible global function definition for 'plot' get.snp.distr.plot: no visible global function definition for 'density' get.snp.distr.plot: no visible global function definition for 'dev.off' grammar: no visible global function definition for 'pchisq' grammar.old: no visible global function definition for 'is' grammar.old: no visible global function definition for 'flush.console' grammar.old: no visible global function definition for 'pchisq' hom: no visible global function definition for 'is' hom.old: no visible global function definition for 'is' ibs: no visible global function definition for 'is' ibs.old: no visible global function definition for 'is' imphetcheck: no visible global function definition for 'is' impute2databel: no visible global function definition for 'get_temporary_file_name' impute2databel: no visible global function definition for 'text2databel' impute2databel: no visible global function definition for 'get_dimnames' impute2databel: no visible global function definition for 'apply2dfo' impute2databel: no visible global function definition for 'databel' impute2databel: no visible global function definition for 'set_dimnames<-' impute2databel: no visible global function definition for 'disconnect' impute2mach: no visible global function definition for 'write.table' impute2mach: no visible global function definition for 'get_dimnames' impute2mach: no visible global function definition for 'as' impute2mach: no visible global function definition for 'disconnect' load.gwaa.data: no visible global function definition for 'read.table' load.gwaa.data: no visible global function definition for 'new' lossFunctionLambdaKS: no visible global function definition for 'ks.test' mach2databel: no visible global function definition for 'get_temporary_file_name' mach2databel: no visible global function definition for 'text2databel' mach2databel: no visible global function definition for 'get_dimnames' makeTransitionMatrix: no visible global function definition for 'is' merge.gwaa.data: no visible global function definition for 'is' merge.gwaa.data: no visible global function definition for 'new' merge.snp.data: no visible global function definition for 'is' merge.snp.data: no visible global function definition for 'write.table' merge.snp.data: no visible global function definition for 'new' minimac2databel: no visible global function definition for 'get_temporary_file_name' minimac2databel: no visible global function definition for 'text2databel' minimac2databel: no visible global function definition for 'get_dimnames' mlreg: no visible global function definition for 'is' mlreg: no visible global function definition for 'model.matrix' mlreg: no visible global function definition for 'model.extract' mlreg: no visible global function definition for 'pchisq' mlreg: no visible global function definition for 'new' mlreg.p: no visible global function definition for 'is' mlreg.p: no visible global function definition for 'model.matrix' mlreg.p: no visible global function definition for 'model.extract' mlreg.p: no visible global function definition for 'pchisq' mmscore: no visible global function definition for 'is' mmscore: no visible global function definition for 'flush.console' mmscore: no visible global function definition for 'pchisq' mmscore: no visible global function definition for 'new' palinear2LiLog: no visible global function definition for 'read.table' palinear2LiLog: no visible global function definition for 'write.table' patch_strand: no visible global function definition for 'new' perid.summary: no visible global function definition for 'is' plot.check.marker: no visible global function definition for 'is' plot.check.marker: no visible global function definition for 'plot' plot.check.marker: no visible global function definition for 'text' plot.check.marker: no visible global function definition for 'lines' plot.check.marker: no visible global function definition for 'points' plot.check.marker: no visible global function definition for 'abline' plot.check.marker: no visible global function definition for 'rug' plot.scan.gwaa: no visible global function definition for 'is' plot.scan.gwaa: no visible global function definition for 'plot' plot.scan.gwaa: no visible global function definition for 'points' plot.scan.gwaa: no visible global function definition for 'axis' plot.scan.gwaa.2D: no visible global function definition for 'image' polygenic: no visible global function definition for 'is' polygenic: no visible global function definition for 'gaussian' polygenic: no visible global function definition for 'binomial' polygenic: no visible global function definition for 'as' polygenic: no visible global function definition for 'model.frame' polygenic: no visible binding for global variable 'na.omit' polygenic: no visible global function definition for 'as.formula' polygenic: no visible global function definition for 'model.response' polygenic: no visible global function definition for 'sd' polygenic: no visible global function definition for 'model.matrix' polygenic: no visible global function definition for 'glm' polygenic: no visible global function definition for 'var' polygenic: no visible global function definition for 'ginv' polygenic: no visible global function definition for 'flush.console' polygenic: no visible global function definition for 'nlm' polygenic: no visible global function definition for 'optim' polygenic: no visible global function definition for 'runif' polygenic_hglm: no visible global function definition for 'gaussian' polygenic_hglm: no visible global function definition for 'is' polygenic_hglm: no visible global function definition for 'as.formula' polygenic_hglm: no visible global function definition for 'model.frame' polygenic_hglm: no visible binding for global variable 'na.omit' polygenic_hglm: no visible global function definition for 'model.response' polygenic_hglm: no visible global function definition for 'model.matrix' polygenic_hglm: no visible global function definition for 'hglm' polygenic_hglm: no visible global function definition for 'ginv' qqplot.plot: no visible global function definition for 'na.omit' qqplot.plot: no visible global function definition for 'rchisq' qqplot.plot: no visible global function definition for 'bitmap' qqplot.plot: no visible global function definition for 'qqplot' qqplot.plot: no visible global function definition for 'abline' qqplot.plot: no visible global function definition for 'dev.off' qqplot.plot: no visible global function definition for 'pchisq' qtscore: no visible global function definition for 'is' qtscore: no visible global function definition for 'as' qtscore: no visible global function definition for 'model.frame' qtscore: no visible binding for global variable 'na.omit' qtscore: no visible global function definition for 'model.response' qtscore: no visible global function definition for 'gaussian' qtscore: no visible global function definition for 'binomial' qtscore: no visible global function definition for 'model.matrix' qtscore: no visible global function definition for 'glm.fit' qtscore: no visible global function definition for 'residuals' qtscore: no visible global function definition for 'txtProgressBar' qtscore: no visible global function definition for 'setTxtProgressBar' qtscore: no visible global function definition for 'pchisq' qtscore: no visible global function definition for 'new' r2fast: no visible global function definition for 'is' r2fast.old: no visible global function definition for 'is' reconstructNPs: no visible global function definition for 'is' redundant: no visible global function definition for 'is' refresh.gwaa.data: no visible global function definition for 'is' refresh.gwaa.data: no visible global function definition for 'new' rhofast: no visible global function definition for 'is' rntransform: no visible binding for global variable 'gaussian' rntransform: no visible global function definition for 'is' rntransform: no visible global function definition for 'as' rntransform: no visible global function definition for 'qnorm' save.gwaa.data: no visible global function definition for 'write.table' save.snp.data: no visible global function definition for 'is' scan.glm: no visible global function definition for 'gaussian' scan.glm: no visible global function definition for 'is' scan.glm: no visible global function definition for 'as.formula' scan.glm: no visible global function definition for 'glm' scan.glm: no visible global function definition for 'anova' scan.glm: no visible global function definition for 'lm' scan.glm: no visible global function definition for 'flush.console' scan.glm: no visible global function definition for 'median' scan.glm: no visible global function definition for 'qchisq' scan.glm.2D: no visible global function definition for 'gaussian' scan.glm.2D: no visible global function definition for 'is' scan.glm.2D: no visible global function definition for 'as.formula' scan.glm.2D: no visible global function definition for 'glm' scan.glm.2D: no visible global function definition for 'anova' scan.glm.2D: no visible global function definition for 'lm' scan.glm.2D: no visible global function definition for 'flush.console' scan.glm.2D: no visible global function definition for 'median' scan.glm.2D: no visible global function definition for 'qchisq' scan.haplo: no visible global function definition for 'is' scan.haplo: no visible global function definition for 'as.formula' scan.haplo: no visible global function definition for 'haplo.score.slide' scan.haplo: no visible global function definition for 'flush.console' scan.haplo: no visible global function definition for 'new' scan.haplo.2D: no visible global function definition for 'is' scan.haplo.2D: no visible global function definition for 'as.formula' scan.haplo.2D: no visible global function definition for 'haplo.score.slide' scan.haplo.2D: no visible global function definition for 'score.sim.control' scan.haplo.2D: no visible global function definition for 'flush.console' show.ncbi: no visible global function definition for 'browseURL' show.ncbi: no visible global function definition for 'is' snp.data: no visible global function definition for 'new' snp.names: no visible global function definition for 'is' snp.names.gwaa.data: no visible global function definition for 'is' snp.subset: no visible global function definition for 'is' snp.subset.scan.gwaa: no visible global function definition for 'new' summary.snp.data: no visible global function definition for 'is' summary.snp.data: no visible global function definition for 'pchisq' summary.snp.data_old: no visible global function definition for 'is' summary.snp.data_old: no visible global function definition for 'pchisq' ztransform: no visible binding for global variable 'gaussian' ztransform: no visible global function definition for 'is' ztransform: no visible global function definition for 'as' ztransform: no visible global function definition for 'model.frame' ztransform: no visible binding for global variable 'na.pass' ztransform: no visible global function definition for 'complete.cases' ztransform: no visible global function definition for 'model.response' ztransform: no visible global function definition for 'model.matrix' ztransform: no visible global function definition for 'glm.fit' ztransform: no visible global function definition for 'sd' [,gwaa.data-ANY-ANY-ANY: no visible global function definition for 'new' [,snp.coding-ANY-missing-missing: no visible global function definition for 'new' [,snp.data-ANY-ANY-ANY: no visible global function definition for 'new' [,snp.mx-ANY-ANY-ANY: no visible global function definition for 'new' [,snp.strand-ANY-missing-missing: no visible global function definition for 'new' coding<-,snp.data: no visible global function definition for 'new' results,scan.gwaa: no visible global function definition for 'pchisq' show,gwaa.data: no visible global function definition for 'show' show,snp.data: no visible global function definition for 'show' Undefined global functions or variables: abline anova apply2dfo as as.dist as.formula axis bartlett.test binomial bitmap boxplot browseURL cmdscale complete.cases databel density dev.off disconnect extract_text_file_columns fisher.test flush.console gaussian genotype get_dimnames get_temporary_file_name ginv glm glm.fit haplo.score.slide hglm image is kmeans kruskal.test ks.test lines lm median model.extract model.frame model.matrix model.response na.omit na.pass new nlm optim optimize par pchisq plot points ppoints qchisq qnorm qqplot quantile qvalue rbinom rchisq read.table residuals rug runif score.sim.control sd setTxtProgressBar set_dimnames<- show t.test text text2databel txtProgressBar var write.table Consider adding importFrom("grDevices", "bitmap", "dev.off") importFrom("graphics", "abline", "axis", "boxplot", "image", "lines", "par", "plot", "points", "rug", "text") importFrom("methods", "as", "is", "new", "show") importFrom("stats", "anova", "as.dist", "as.formula", "bartlett.test", "binomial", "cmdscale", "complete.cases", "density", "fisher.test", "gaussian", "glm", "glm.fit", "kmeans", "kruskal.test", "ks.test", "lm", "median", "model.extract", "model.frame", "model.matrix", "model.response", "na.omit", "na.pass", "nlm", "optim", "optimize", "pchisq", "ppoints", "qchisq", "qnorm", "qqplot", "quantile", "rbinom", "rchisq", "residuals", "runif", "sd", "t.test", "var") importFrom("utils", "browseURL", "flush.console", "read.table", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 line endings in Makefiles ... NOTE Found the following Makefile(s) without a final LF: inst/unitTests/Makefile Some 'make' programs ignore lines not ending in LF. * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking examples ... ** running examples for arch 'i386' ... [54s] OK ** running examples for arch 'x64' ... [59s] OK * checking PDF version of manual ... OK * DONE Status: 6 NOTEs