* using log directory 'd:/Rcompile/CRANpkg/local/2.11/phyclust.Rcheck' * using R version 2.11.1 Patched (2010-07-29 r52657) * using session charset: ISO8859-1 * checking for file 'phyclust/DESCRIPTION' ... OK * this is package 'phyclust' version '0.1-8' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'phyclust' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level 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 name space can be loaded with stated dependencies ... OK * checking whether the name space can be unloaded cleanly ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE chkdim.Add.fun: no visible binding for global variable 'RRstar' get.deriBigMatB.fun: no visible binding for global variable 'k' get.fullBB.fun: no visible binding for global variable 'medBB.cs' get.fullBB.fun: no visible binding for global variable 'subPI.cs' get.matD.matEI.fun: no visible binding for global variable 'y' get.matD.matEI.fun: no visible binding for global variable 'mu' get.matD.matEI.fun: no visible binding for global variable 'a' get.matD.matEI.fun: no visible binding for global variable 'xRD.post' get.matD.matEI.fun: no visible binding for global variable 'x.post' get.matD.matEI.fun: no visible binding for global variable 'xRD' get.matD.matEI.fun: no visible binding for global variable 'x' get.matD.matEI.fun: no visible binding for global variable 'post' get.matD.matEI.fun: no visible binding for global variable 'v' get.matD.matEI.fun: no visible binding for global variable 'nreps' get.matD.matEI.fun: no visible binding for global variable 'CC' get.matD.matEI.fun: no visible binding for global variable 'subPI' get.matD.matEI.fun: no visible binding for global variable 'BB' get.matD.matEI.fun: no visible binding for global variable 'p.cscn.FD' get.matD.matEI.fun: no visible binding for global variable 'x.adj' get.medBB.skip.fun: no visible binding for global variable 'subPI.cn' get.medBB.skip.fun: no visible binding for global variable 'preBB.cn' get.medBB.skip.fun: no visible binding for global variable 'indexBB.cn' get.preBB.skip.fun: no visible binding for global variable 'subPI.cs' getBigMatB.fun: no visible binding for global variable 'BB.cs' getBigMatB.fun: no visible binding for global variable 'subPI.cs' getI13.fun: no visible binding for global variable 'y' getPIstar.fun: no visible binding for global variable 'BB.cs' getPIstar.fun: no visible binding for global variable 'subPI.cs' getcut.fun: no visible binding for global variable 'nhap' haplo.score.RD.unphased.fun: no visible binding for global variable 'Y.vec' haplo.score.RD.unphased.fun: no visible binding for global variable 'Geno' haplo.score.RD.unphased.fun: no visible global function definition for 'haplo.em' haplo.score.RD.unphased.fun: no visible global function definition for 'haplo.em.control' haplo.score.RD.unphased.fun: no visible binding for global variable 'nhap' haplo.score.RD.unphased.fun: no visible binding for global variable 'digit' haplo.score.RD.unphased.fun: no visible global function definition for 'Ginv' * 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 data for non-ASCII characters ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for portable compilation flags in Makevars ... OK * checking for portable use of $BLAS_LIBS ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * checking PDF version of manual ... OK