Package: CGHnormaliter

Version: 1.7.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings CGHnormaliter_1.7.0.tar.gz

StartedAt: 2011-05-09 12:57:35 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:59:45 -0700 (Mon, 09 May 2011)

EllapsedTime: 129.7 seconds

RetCode: 0

Status:  OK

CheckDir: CGHnormaliter.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/CGHnormaliter.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGHnormaliter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHnormaliter' version '1.7.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'CGHnormaliter' 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
* 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 ... 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 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 'CGHnormaliter' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: impute
Loading required package: DNAcopy

**************************************************************************
   The plan to change the data format for CNA object has been postponed   
 in order to ensure backward compatibility with older versions of DNAcopy 
**************************************************************************

Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: CGHbase
Loading required package: marray
Loading required package: limma

Attaching package: 'CGHcall'

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

    bpend, bpstart, calls, calls<-, chromosomes, copynumber,
    copynumber<-, probamp, probamp<-, probgain, probgain<-, probloss,
    probloss<-, probnorm, probnorm<-, segmented, segmented<-

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'CGHnormaliter.Rnw' 
Warning: value of 'results' option should be lowercase
Warning: value of 'results' option should be lowercase
** testing if installed package can be loaded

* DONE (CGHnormaliter)

name	user	system	elapsed
CGHnormaliter	63.51	0.03	64.58
CGHnormaliter.write.table	0.59	0.00	0.60