Package: beadarraySNP

Version: 1.14.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings beadarraySNP_1.14.0.tar.gz

StartedAt: 2010-10-04 16:09:07 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 16:09:59 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 51.5 seconds

RetCode: 0

Status:  OK

CheckDir: beadarraySNP.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/beadarraySNP.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.14.0'
* 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 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 '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 (0.86) 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	3.744	0.092	3.871
PolarTransforms	0.012	0.004	0.016
SnpSetSegments-class	0.000	0.000	0.001
backgroundCorrect.SNP	0	0	0
calculateQCarray	0.000	0.000	0.001
compareGenotypes	0.004	0.004	0.007
dist.GT	0.068	0.016	0.086
heterozygosity	0.032	0.000	0.032
heterozygousSNPs	0.096	0.000	0.096
normalizeBetweenAlleles.SNP	0.084	0.000	0.084
normalizeBetweenSubsamples.SNP	0.056	0.000	0.055
normalizeLoci.SNP	0.028	0.000	0.030
normalizeWithinArrays.SNP	0.04	0.00	0.04
pdfChromosomesSmoothCopyNumber	0	0	0
plotQC	0.004	0.000	0.005
read.SnpSetIllumina	1.380	0.020	1.401
removeLowQualitySamples	0.048	0.000	0.047
reportSamplePanelQC-methods	0.012	0.000	0.010
standardNormalization	0.148	0.000	0.147