Package: CGHcall

Version: 2.13.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CGHcall_2.13.0.tar.gz

StartedAt: 2011-05-09 13:48:28 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 13:50:02 -0700 (Mon, 09 May 2011)

EllapsedTime: 93.5 seconds

RetCode: 0

Status:  OK

CheckDir: CGHcall.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/CGHcall.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGHcall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHcall’ version ‘2.13.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘CGHcall’ 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 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘CGHcall.pdf’ from 826Kb to 134Kb
  consider running tools::compactPDF() on these files
* 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 ‘CGHcall’ ...
** R
** data
** inst
** preparing package for lazy loading

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


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: marray
Loading required package: limma
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘CGHcall.Rnw’ 
** testing if installed package can be loaded

* DONE (CGHcall)

name	user	system	elapsed
CGHcall	1.381	0.210	2.008
ExpandCGHcall	1.213	0.195	1.442
class.cghCall	0.106	0.001	0.107
class.cghRaw	0.627	0.077	0.708
class.cghSeg	0.103	0.002	0.104
make_cghRaw	0.153	0.009	0.161
normalize	1.239	0.192	1.530
plot.summary	0.000	0.000	0.001
postsegnormalize	1.297	0.242	1.891
preprocess	0.107	0.006	0.246
segmentData	0.025	0.002	0.042