* using log directory 'd:/Rcompile/CRANpkg/local/3.1/iteRates.Rcheck' * using R version 3.1.3 (2015-03-09) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'iteRates/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'iteRates' version '3.1' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'partitions' 'VGAM' 'MASS' 'ape' 'apTreeshape' 'geiger' 'gtools' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 'iteRates' 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 dependencies in R code ... NOTE Packages in Depends field not imported from: 'MASS' 'VGAM' 'apTreeshape' 'ape' 'geiger' 'gtools' 'partitions' 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 BOTHlabels2: no visible global function definition for 'floating.pie.asp' PosGroups: no visible global function definition for 'combinations' Qcomp.subs: no visible global function definition for 'branching.times' birthdeath.tree.geiger1.3.1: no visible global function definition for 'old2new.phylo' birthdeath.tree.geiger1.3.1: no visible global function definition for 'read.tree' birthdeath.tree.geiger1.3.1: no visible global function definition for 'write.tree' comBim: no visible global function definition for 'restrictedparts' comp.subs: no visible global function definition for 'branching.times' comp.subs.DF: no visible global function definition for 'branching.times' compareSubTrees: no visible global function definition for 'branching.times' drop.tip2.6: no visible global function definition for 'is.rooted' drop.tip2.6: no visible binding for global variable '.PlotPhyloEnv' drop.tip2.6: no visible global function definition for 'root' drop.tip2.6: no visible global function definition for 'collapse.singles' edgelabels2: no visible binding for global variable '.PlotPhyloEnv' internds: no visible global function definition for 'branching.times' plot.phylo2: no visible global function definition for 'unrooted.xy' plot.phylo2: no visible global function definition for 'circular.plot' plot.phylo2: no visible global function definition for 'cladogram.plot' plot.phylo2: no visible binding for global variable '.PlotPhyloEnv' subtrees2.6: no visible global function definition for 'Ntip' subtrees2.6: no visible global function definition for 'Nnode' subtrees2.6: no visible global function definition for 'drop.tip' subtreez: no visible global function definition for 'Ntip' subtreez: no visible global function definition for 'Nnode' tree.rand.test: no visible global function definition for 'branching.times' trimTree: no visible global function definition for 'is.ultrametric' trimTree: no visible global function definition for 'branching.times' trimTree: no visible global function definition for 'multi2di' trimTree: no visible global function definition for 'read.tree' trimTree: no visible global function definition for 'write.tree' * 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 examples ... [6s] OK * checking PDF version of manual ... OK * DONE NOTE: There were 3 notes.