Check results for 'TAHMMAnnot'

using R Under development (unstable) (2012-05-19 r59366)
using platform: x86_64-unknown-linux-gnu (64-bit)
using session charset: UTF-8
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 ... WARNING
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 for executable files ... OK
checking whether package ‘TAHMMAnnot’ can be installed ... OK
checking installed package size ... OK
checking package directory ... OK
checking for portable file names ... OK
checking for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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
WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/TAHMMAnnot.Rcheck/00check.log’
for details.