Package: beadarraySNP

Version: 1.16.0

Command: D:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings beadarraySNP_1.16.0.tar.gz

StartedAt: 2011-04-07 08:54:27 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 08:56:07 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 99.9 seconds

RetCode: 0

Status:  OK

CheckDir: beadarraySNP.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.7-bioc/meat/beadarraySNP.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.16.0'
* 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 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... 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
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: quantreg
Loading required package: SparseM
Package SparseM (0.87) 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 ...
** testing if installed package can be loaded

* DONE (beadarraySNP)

name	user	system	elapsed
GenomicReports	4.53	0.10	4.74
PolarTransforms	0.03	0.00	0.03
SnpSetSegments-class	0	0	0
backgroundCorrect.SNP	0	0	0
calculateQCarray	0	0	0
compareGenotypes	0	0	0
dist.GT	0.08	0.01	0.09
heterozygosity	0.03	0.00	0.03
heterozygousSNPs	0.09	0.00	0.10
normalizeBetweenAlleles.SNP	0.05	0.02	0.06
normalizeBetweenSubsamples.SNP	0.05	0.00	0.05
normalizeLoci.SNP	0.03	0.00	0.03
normalizeWithinArrays.SNP	0.05	0.00	0.04
pdfChromosomesSmoothCopyNumber	0	0	0
plotQC	0	0	0
read.SnpSetIllumina	1.43	0.00	1.44
removeLowQualitySamples	0.05	0.00	0.05
reportSamplePanelQC-methods	0.02	0.00	0.01
standardNormalization	0.11	0.02	0.13