Package: beadarraySNP

Version: 1.25.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings beadarraySNP_1.25.0.tar.gz

StartedAt: 2013-03-25 00:14:23 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:16:04 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 101.7 seconds

RetCode: 0

Status:  OK

CheckDir: beadarraySNP.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/beadarraySNP.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘1.25.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘beadarraySNP’ can be installed ... [7s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
plotQC,QCIllumina: warning in rgb(0, 0:255, 0, max = 255): partial
  argument match of 'max' to 'maxColorValue'
plotQC,QCIllumina: warning in rgb(0:255, 0, 0, max = 255): partial
  argument match of 'max' to 'maxColorValue'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
  colstart:colend, maxColorValue = colend): partial argument match of
  'r' to 'red'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
  colstart:colend, maxColorValue = colend): partial argument match of
  'g' to 'green'
reportSamplePanelQC,QCIllumina: warning in rgb(r = 0, b = 0, g =
  colstart:colend, maxColorValue = colend): partial argument match of
  'b' to 'blue'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
  0, g = 0, maxColorValue = colend): partial argument match of 'r' to
  'red'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
  0, g = 0, maxColorValue = colend): partial argument match of 'g' to
  'green'
reportSamplePanelQC,QCIllumina: warning in rgb(r = colstart:colend, b =
  0, g = 0, maxColorValue = colend): partial argument match of 'b' to
  'blue'
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 installed files from ‘inst/doc’ ... OK
* checking examples ... [9s/9s] 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/beadarraySNP.Rcheck/00check.log’
for details.

* installing *source* package ‘beadarraySNP’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘beadarraySNP.rnw’ 
** testing if installed package can be loaded
* DONE (beadarraySNP)

name	user	system	elapsed
GenomicReports	4.220	0.068	4.322
PolarTransforms	0.032	0.000	0.033
SnpSetSegments-class	0.020	0.000	0.021
backgroundCorrect.SNP	0.144	0.000	0.149
calculateQCarray	0.012	0.000	0.009
compareGenotypes	0.016	0.004	0.020
dist.GT	0.124	0.004	0.132
heterozygosity	0.048	0.000	0.081
heterozygousSNPs	0.112	0.004	0.113
normalizeBetweenAlleles.SNP	0.068	0.004	0.072
normalizeBetweenSubsamples.SNP	0.052	0.000	0.051
normalizeLoci.SNP	0.044	0.000	0.043
normalizeWithinArrays.SNP	0.040	0.000	0.042
pdfChromosomesSmoothCopyNumber	0.012	0.000	0.010
plotQC	0.016	0.000	0.017
read.SnpSetIllumina	1.276	0.004	1.295
removeLowQualitySamples	0.056	0.000	0.057
reportSamplePanelQC-methods	0.028	0.004	0.032
standardNormalization	0.124	0.004	0.130