BioC 2.13: CHECK report for beadarraySNP on perceval

Package: beadarraySNP

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarraySNP_1.28.0.tar.gz

StartedAt: 2014-04-04 23:40:09 -0700 (Fri, 04 Apr 2014)

EndedAt: 2014-04-04 23:41:40 -0700 (Fri, 04 Apr 2014)

EllapsedTime: 91.7 seconds

RetCode: 0

Status:  OK

CheckDir: beadarraySNP.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/beadarraySNP.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.28.0’
* 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 ... [6s/6s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘getMidMaxIdx’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘beadarraySNP.rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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
** testing if installed package can be loaded
* DONE (beadarraySNP)

name	user	system	elapsed
GenomicReports	4.209	0.190	4.593
PolarTransforms	0.027	0.003	0.048
SnpSetSegments-class	0.007	0.001	0.007
backgroundCorrect.SNP	0.006	0.000	0.017
calculateQCarray	0.005	0.002	0.016
compareGenotypes	0.011	0.002	0.012
dist.GT	0.103	0.017	0.137
heterozygosity	0.043	0.002	0.049
heterozygousSNPs	0.107	0.003	0.122
normalizeBetweenAlleles.SNP	0.089	0.003	0.106
normalizeBetweenSubsamples.SNP	0.068	0.002	0.089
normalizeLoci.SNP	0.036	0.001	0.037
normalizeWithinArrays.SNP	0.032	0.002	0.034
pdfChromosomesSmoothCopyNumber	0.008	0.001	0.008
plotQC	0.014	0.002	0.016
read.SnpSetIllumina	1.303	0.023	1.422
removeLowQualitySamples	0.040	0.004	0.046
reportSamplePanelQC-methods	0.017	0.005	0.024
standardNormalization	0.124	0.006	0.132