Package: cghMCR

Version: 1.12.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch cghMCR_1.12.0.tar.gz

StartedAt: 2012-01-09 01:54:29 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 01:56:43 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 133.9 seconds

RetCode: 0

Status:  OK

CheckDir: cghMCR.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/cghMCR.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cghMCR/DESCRIPTION' ... OK
* this is package 'cghMCR' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'cghMCR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 98.7Mb
  sub-directories of 1Mb or more:
    sampleData  97.1Mb
* 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 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 ... NOTE
prepare_Rd: SGOL-class.Rd:49: Dropping empty section \note
prepare_Rd: cghMCR-class.Rd:56: Dropping empty section \references
prepare_Rd: mergeMCRProbes.Rd:28: 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.DNAcopy':
  'plot.DNAcopy'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'cghMCR' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in library.dynam("CNTools", package = "CNTools") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated
Creating a generic function for 'print' from package 'base' in package 'cghMCR'
Creating a generic function for 'colnames' from package 'base' in package 'cghMCR'
Creating a generic function for 'rownames' from package 'base' in package 'cghMCR'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'findMCR.Rnw' 
** testing if installed package can be loaded
Warning in library.dynam("CNTools", package = "CNTools") :
  use of library.dynam() without specifying both 'package' and 'lib.loc' is deprecated

* DONE (cghMCR)

name	user	system	elapsed
SGOL-class	0	0	0
cghMCR-class	0.11	0.00	0.25
cghMCR	0.22	0.00	0.22
mergeMCRProbes	5.21	0.02	5.22
plot.DNAcopy	0	0	0