* using log directory 'd:/Rcompile/CRANpkg/local/3.3/mpMap.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 'mpMap/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'mpMap' version '1.14' * checking package namespace information ... OK * checking package dependencies ... NOTE Packages suggested but not available for checking: 'asreml' 'happy.hbrem' * 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 'mpMap' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 to packages already attached by Depends: 'gdata' 'seriation' Please remove these calls from your code. 'library' or 'require' calls in package code: 'Heatplus' 'VPdtw' 'aod' 'asreml' 'happy.hbrem' 'lattice' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'gdata' 'seriation' 'wgaim' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': 'qtl:::readMWril' See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: 'qtl:::adjust.rf.ri' 'qtl:::plot.scanone' 'qtl:::ripple.perm1' 'qtl:::ripple.perm2' 'qtl:::testchr' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... NOTE Foreign function calls to a different package: .C("R_reorgRIgenoprob", ..., PACKAGE = "qtl") .C(cfunc, ..., PACKAGE = "qtl") .C(func, ..., PACKAGE = "qtl") See chapter 'System and foreign language interfaces' in the 'Writing R Extensions' manual. * checking R code for possible problems ... NOTE CR_calcLD: no visible global function definition for 'lowerTriangle' calc.genoprob2: no visible binding for global variable 'step' cintern : : no visible global function definition for 'contr.helmert' cintern: no visible global function definition for 'pchisq' fill: no visible global function definition for 'upperTriangle<-' fill: no visible global function definition for 'lowerTriangle<-' fill: no visible global function definition for 'lowerTriangle' fill: no visible global function definition for 'upperTriangle' findqtl2: no visible global function definition for 'dilation' fit.mpqtl: no visible global function definition for 'update' fit.mpqtl: no visible global function definition for 'as.formula' fit.mpqtl: no visible global function definition for 'coef' fit.mpqtl: no visible global function definition for 'wald.test' fit.mpqtl: no visible global function definition for 'vcov' gen8ped: no visible global function definition for 'combn' generate_obs: no visible global function definition for 'runif' generate_pheno: no visible global function definition for 'rnorm' getpval: no visible global function definition for 'pf' mapcomp: no visible global function definition for 'cor' mpIM: no visible global function definition for 'update' mpIM: no visible global function definition for 'na.omit' mpIM: no visible global function definition for 'as.formula' mpIM: no visible global function definition for 'lm' mpIM: no visible global function definition for 'stepAIC' mpIM: no visible global function definition for 'coef' mpIM: no visible global function definition for 'wald.test' mpIM: no visible global function definition for 'vcov' mpcalcld: no visible global function definition for 'combn' mpcalcld: no visible global function definition for 'lowerTriangle<-' mpcalcld: no visible global function definition for 'upperTriangle<-' mpcalcld: no visible global function definition for 'upperTriangle' mpestrf: no visible global function definition for 'combn' mpestrf: no visible global function definition for 'lowerTriangle<-' mpestrf: no visible global function definition for 'upperTriangle<-' mpestrf: no visible global function definition for 'upperTriangle' mporder: no visible global function definition for 'as.dist' mporder : : no visible global function definition for 'seriate' mporder: no visible binding for global variable 'get_order' mpprob: no visible global function definition for 'happy' mpprob: no visible global function definition for 'hdesign' mpsegrat: no visible global function definition for 'pchisq' plot.mapcomp: no visible global function definition for 'xyplot' plot.mpcross: no visible global function definition for 'par' plot.mpcross: no visible global function definition for 'hist' plot.mpcross: no visible global function definition for 'plot' plot.mpcross: no visible global function definition for 'upperTriangle<-' plot.mpcross: no visible global function definition for 'upperTriangle' plot.mpcross: no visible global function definition for 'lowerTriangle<-' plot.mpcross: no visible global function definition for 'lowerTriangle' plot.mpcross: no visible global function definition for 'heatmap_2' plot.mpprob: no visible global function definition for 'barplot' plot.mpprob: no visible global function definition for 'par' plot.mpprob: no visible global function definition for 'heatmap' plot.mpqtl: no visible global function definition for 'rect' plotlink.map: no visible global function definition for 'par' plotlink.map: no visible global function definition for 'plot' plotlink.map: no visible global function definition for 'axis' plotlink.map: no visible global function definition for 'text' plotlink.map: no visible global function definition for 'segments' plotlink.map: no visible global function definition for 'lines' plotlink.map: no visible global function definition for 'title' read.mpcross: no visible global function definition for 'read.table' sim.sigthr: no visible global function definition for 'var' sim.sigthr: no visible global function definition for 'rnorm' supportinterval: no visible global function definition for 'qchisq' supportinterval: no visible global function definition for 'pchisq' wald.test.asreml: no visible global function definition for 'update' write2cross: no visible global function definition for 'rnorm' write2cross: no visible global function definition for 'write.csv' write2cross: no visible global function definition for 'write.table' write2happy: no visible global function definition for 'write.table' Undefined global functions or variables: as.dist as.formula axis barplot coef combn contr.helmert cor dilation get_order happy hdesign heatmap heatmap_2 hist lines lm lowerTriangle lowerTriangle<- na.omit par pchisq pf plot qchisq read.table rect rnorm runif segments seriate step stepAIC text title update upperTriangle upperTriangle<- var vcov wald.test write.csv write.table xyplot Consider adding importFrom("graphics", "axis", "barplot", "hist", "lines", "par", "plot", "rect", "segments", "text", "title") importFrom("stats", "as.dist", "as.formula", "coef", "contr.helmert", "cor", "heatmap", "lm", "na.omit", "pchisq", "pf", "qchisq", "rnorm", "runif", "step", "update", "var", "vcov") importFrom("utils", "combn", "read.table", "write.csv", "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 examples ... ** running examples for arch 'i386' ... [21s] OK ** running examples for arch 'x64' ... [24s] OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs