* using log directory 'd:/Rcompile/CRANpkg/local/2.15/TAHMMAnnot.Rcheck' * using R version 2.15.0 (2012-03-30) * using platform: x86_64-pc-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'TAHMMAnnot/DESCRIPTION' ... OK * this is package 'TAHMMAnnot' version '1.0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... NOTE As from R 2.14.0 all packages need a namespace. One will be generated on installation, but it is better to handcraft a NAMESPACE file: R CMD build will produce a suitable starting point. CRAN requires a NAMESPACE file for all submissions. * checking whether package 'TAHMMAnnot' can be installed ... OK * checking installed package size ... 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 * 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 * 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 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 File 'TAHMMAnnot/R/zzz.R': .First.lib calls: cat("TAHMMAnnot Loaded \n") Package startup functions should use 'packageStartupMessage' to generate messages. See section 'Good practice' in ?.onAttach. Bidim_Gaussian_Mixture: warning in read.table(fileIN, h = header, sep = sep, ...): partial argument match of 'h' to 'header' HMM: warning in read.table(fileIN, h = header, sep = sep, ...): partial argument match of 'h' to 'header' HMM_Annot: warning in read.table(fileIN, h = header, sep = sep, ...): partial argument match of 'h' to 'header' HMM_Annot_restart0: warning in read.table(fileIN, h = header, sep = sep, ...): partial argument match of 'h' to 'header' Mixture_Annot: warning in read.table(fileIN, h = header, sep = sep, ...): partial argument match of 'h' to 'header' Normalisation_ANOVA: warning in read.table(fileIN, h = TRUE): partial argument match of 'h' to 'header' Process_norm: warning in read.table(fileOUT, h = TRUE): partial argument match of 'h' to 'header' Sort_file: warning in read.table(fileIN, h = TRUE): partial argument match of 'h' to 'header' normalisation_lowess: warning in read.table(paste(file[i, 1], "_532.pair", sep = ""), h = TRUE, skip = 1, sep = sep.read): partial argument match of 'h' to 'header' normalisation_lowess: warning in read.table(paste(file[i, 1], "_635.pair", sep = ""), h = TRUE, skip = 1, sep = sep.read): partial argument match of 'h' to 'header' normalisation_lowess: warning in read.table(file[grep(name.chr[n], file)[1]], h = TRUE): partial argument match of 'h' to 'header' normalisation_lowess: warning in read.table(file[grep(name.chr[n], file)[2]], h = TRUE): partial argument match of 'h' to 'header' * checking Rd files ... NOTE prepare_Rd: Acces.Rd:15-17: Dropping empty section \details prepare_Rd: Acces.Rd:21-23: Dropping empty section \references prepare_Rd: Acces.Rd:25: Dropping empty section \seealso prepare_Rd: BackwardAnnotR.Rd:19-21: Dropping empty section \details prepare_Rd: BackwardAnnotR.Rd:26-28: Dropping empty section \references prepare_Rd: BackwardAnnotrestart0R.Rd:20-22: Dropping empty section \details prepare_Rd: BackwardAnnotrestart0R.Rd:27-29: Dropping empty section \references prepare_Rd: BackwardR.Rd:16-18: Dropping empty section \details prepare_Rd: BackwardR.Rd:23-25: Dropping empty section \references prepare_Rd: Bidim_Gaussian_Mixture.Rd:66: Dropping empty section \keyword prepare_Rd: Bidim_Gaussian_Mixture.Rd:67: Dropping empty section \keyword prepare_Rd: Bidim_Gaussian_Mixture_allchr.Rd:61: Dropping empty section \keyword prepare_Rd: Bidim_Gaussian_Mixture_allchr.Rd:62: Dropping empty section \keyword prepare_Rd: CalculDirect.Rd:13-15: Dropping empty section \details prepare_Rd: CalculDirect.Rd:19-21: Dropping empty section \references prepare_Rd: ForwardAnnotR.Rd:19-21: Dropping empty section \details prepare_Rd: ForwardAnnotR.Rd:25-27: Dropping empty section \references prepare_Rd: ForwardAnnotrestart0R.Rd:20-22: Dropping empty section \details prepare_Rd: ForwardAnnotrestart0R.Rd:26-28: Dropping empty section \references prepare_Rd: ForwardR.Rd:17-19: Dropping empty section \details prepare_Rd: ForwardR.Rd:23-25: Dropping empty section \references prepare_Rd: HMM.Rd:68: Dropping empty section \keyword prepare_Rd: HMM.Rd:69: Dropping empty section \keyword prepare_Rd: HMM_Annot.Rd:71: Dropping empty section \keyword prepare_Rd: HMM_Annot_allchr.Rd:64: Dropping empty section \keyword prepare_Rd: HMM_Annot_allchr.Rd:65: Dropping empty section \keyword prepare_Rd: HMM_Annot_restart0.Rd:73: Dropping empty section \keyword prepare_Rd: HMM_Annot_restart0_allchr.Rd:64: Dropping empty section \keyword prepare_Rd: HMM_Annot_restart0_allchr.Rd:65: Dropping empty section \keyword prepare_Rd: HMM_allchr.Rd:64: Dropping empty section \keyword prepare_Rd: HMM_allchr.Rd:65: Dropping empty section \keyword prepare_Rd: Initialization.Rd:15-17: Dropping empty section \details prepare_Rd: Initialization.Rd:21-23: Dropping empty section \references prepare_Rd: Initialization.Rd:25: Dropping empty section \seealso prepare_Rd: Mixture_Annot.Rd:70: Dropping empty section \keyword prepare_Rd: Mixture_Annot_allchr.Rd:65: Dropping empty section \keyword prepare_Rd: Mixture_Annot_allchr.Rd:66: Dropping empty section \keyword prepare_Rd: Normalisation_ANOVA.Rd:31: Dropping empty section \keyword prepare_Rd: Normalisation_ANOVA.Rd:32: Dropping empty section \keyword prepare_Rd: Normalisation_ANOVA.Rd:25-27: Dropping empty section \references prepare_Rd: Normalisation_ANOVA.Rd:29: Dropping empty section \seealso prepare_Rd: Process_norm.Rd:51: Dropping empty section \keyword prepare_Rd: Process_norm.Rd:52: Dropping empty section \keyword prepare_Rd: Process_norm.Rd:45-47: Dropping empty section \references prepare_Rd: ProdMat.Rd:15-17: Dropping empty section \details prepare_Rd: ProdMat.Rd:21-23: Dropping empty section \references prepare_Rd: ProdMat.Rd:25: Dropping empty section \seealso prepare_Rd: ProdMat2.Rd:14-16: Dropping empty section \details prepare_Rd: ProdMat2.Rd:20-22: Dropping empty section \references prepare_Rd: ProdMat2.Rd:24: Dropping empty section \seealso prepare_Rd: ProdMatGauss.Rd:14-16: Dropping empty section \details prepare_Rd: ProdMatGauss.Rd:20-22: Dropping empty section \references prepare_Rd: ProdMatGauss.Rd:24: Dropping empty section \seealso prepare_Rd: Sort_file.Rd:21-23: Dropping empty section \references prepare_Rd: Sort_file.Rd:25: Dropping empty section \seealso prepare_Rd: Tau.Rd:16-18: Dropping empty section \details prepare_Rd: Tau.Rd:22-24: Dropping empty section \references prepare_Rd: Tauannot.Rd:16-18: Dropping empty section \details prepare_Rd: Tauannot.Rd:22-24: Dropping empty section \references prepare_Rd: matW.Rd:21-23: Dropping empty section \references prepare_Rd: matW.Rd:25: Dropping empty section \seealso prepare_Rd: normalisation_lowess.Rd:34: Dropping empty section \keyword prepare_Rd: normalisation_lowess.Rd:35: Dropping empty section \keyword prepare_Rd: normalisation_lowess.Rd:28-30: Dropping empty section \references * 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 ... OK * checking for portable compilation flags in Makevars ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking examples ... NONE * checking PDF version of manual ... OK NOTE: There were 3 notes. See 'd:/Rcompile/CRANpkg/local/2.15/TAHMMAnnot.Rcheck/00check.log' for details.