Package: CGHnormaliter

Version: 1.2.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings CGHnormaliter_1.2.0.tar.gz

StartedAt: 2010-10-04 16:38:04 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:39:20 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 75.9 seconds

RetCode: 0

Status:  OK

CheckDir: CGHnormaliter.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/CGHnormaliter.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGHnormaliter/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CGHnormaliter' version '1.2.0'
* 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 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 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'CGHnormaliter' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: impute
Loading required package: DNAcopy

**************************************************************************
   The data format for the CNA object will be changed in version 1.23.0 
     Instead of a data frame it will be a list of 3 (or more) objects 
     chrom and maploc will be vectors and CN/LOH data will be a matrix 
**************************************************************************

Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. 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 ...
** testing if installed package can be loaded

* DONE (CGHnormaliter)

name	user	system	elapsed
CGHnormaliter	34.286	0.304	35.768
CGHnormaliter.write.table	0.740	0.012	0.753