Package: beadarraySNP

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarraySNP_1.19.0.tar.gz

StartedAt: 2011-06-22 01:33:33 -0700 (Wed, 22 Jun 2011)

EndedAt: 2011-06-22 01:35:41 -0700 (Wed, 22 Jun 2011)

EllapsedTime: 127.9 seconds

RetCode: 0

Status:  OK

CheckDir: beadarraySNP.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/beadarraySNP.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarraySNP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘beadarraySNP’ version ‘1.19.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘beadarraySNP’ 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 ... NOTE
read.SnpSetIllumina: no visible global function definition for
  ‘createBeadSummaryData’
* 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’ ... 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 ‘beadarraySNP’ ...
** R
** data
** inst
** preparing package for lazy loading

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: quantreg
Loading required package: SparseM
Package SparseM (0.89) loaded.
	   To cite, see citation("SparseM")


Attaching package: ‘SparseM’

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

    backsolve

Loading required package: lodplot
Loading required package: grid
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘beadarraySNP.rnw’ 
** testing if installed package can be loaded

* DONE (beadarraySNP)

name	user	system	elapsed
GenomicReports	6.105	0.684	12.122
PolarTransforms	0.026	0.003	0.059
SnpSetSegments-class	0.003	0.000	0.004
backgroundCorrect.SNP	0.000	0.000	0.009
calculateQCarray	0.001	0.000	0.000
compareGenotypes	0.013	0.002	0.014
dist.GT	0.125	0.010	0.186
heterozygosity	0.055	0.001	0.107
heterozygousSNPs	0.132	0.002	0.216
normalizeBetweenAlleles.SNP	0.101	0.007	0.217
normalizeBetweenSubsamples.SNP	0.072	0.004	0.118
normalizeLoci.SNP	0.046	0.005	0.098
normalizeWithinArrays.SNP	0.050	0.003	0.103
pdfChromosomesSmoothCopyNumber	0.000	0.000	0.001
plotQC	0.008	0.000	0.008
read.SnpSetIllumina	1.039	0.022	1.972
removeLowQualitySamples	0.063	0.003	0.117
reportSamplePanelQC-methods	0.015	0.001	0.026
standardNormalization	0.187	0.014	0.367