Package: beadarraySNP

Version: 1.20.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch beadarraySNP_1.20.0.tar.gz

StartedAt: 2012-01-09 01:26:55 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 01:27:59 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 63.8 seconds

RetCode: 0

Status:  OK

CheckDir: beadarraySNP.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/beadarraySNP.Rcheck'
* using R version 2.14.1 (2011-12-22)
* 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 '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 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
** 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	4.28	0.03	4.50
PolarTransforms	0.03	0.00	0.04
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	0.07	0.00	0.07
normalizeBetweenAlleles.SNP	0.04	0.02	0.05
normalizeBetweenSubsamples.SNP	0.04	0.00	0.05
normalizeLoci.SNP	0.02	0.00	0.01
normalizeWithinArrays.SNP	0.03	0.00	0.03
pdfChromosomesSmoothCopyNumber	0	0	0
plotQC	0.01	0.00	0.02
read.SnpSetIllumina	1.41	0.00	1.41
removeLowQualitySamples	0.05	0.00	0.04
reportSamplePanelQC-methods	0.01	0.00	0.02
standardNormalization	0.08	0.01	0.09