* using log directory 'd:/Rcompile/CRANpkg/local/2.13/ExomeDepth.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'ExomeDepth/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ExomeDepth' version '0.7.3'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ExomeDepth' 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
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace 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 whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace 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 ... OK
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under inst/doc ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... WARNING
Errors in running code in vignettes:
when running code in 'ExomeDepth-vignette.Rnw'
  ...
Loading required package: Biostrings

> data(ExomeCount)

> ExomeCount <- as(ExomeCount[, colnames(ExomeCount)], 
+     "data.frame")

  When sourcing 'ExomeDepth-vignette.R':
Error: no method or default for coercing "RangedData" to "data.frame"
Execution halted

* checking re-building of vignettes ... NOTE
Error in re-building vignettes:
  ...
    biplot, case.names, coef, coefficients, df.residual, fitted,
    fitted.values, formula, poly, residuals, variable.names, weights

The following object(s) are masked from 'package:base':

    identity, scale.default

Loading required package: GenomicRanges
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: Rsamtools
Loading required package: Biostrings

Error: processing vignette 'ExomeDepth-vignette.Rnw' failed with diagnostics:
 chunk 1 (label = Rsamtools.load) 
Error in as(ExomeCount[, colnames(ExomeCount)], "data.frame") : 
  no method or default for coercing "RangedData" to "data.frame"
Execution halted

* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
  'd:/Rcompile/CRANpkg/local/2.13/ExomeDepth.Rcheck/00check.log'
for details