BioC 2.14: CHECK report for beadarraySNP on petty

Package: beadarraySNP

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarraySNP_1.30.0.tar.gz

StartedAt: 2014-10-07 20:51:05 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 20:53:04 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 119.5 seconds

RetCode: 0

Status:  OK

CheckDir: beadarraySNP.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarraySNP_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/beadarraySNP.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.30.0’
* 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 ‘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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... [11s/13s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
GenomicReports 5.317  0.224   5.711
* 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 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	5.317	0.224	5.711
PolarTransforms	0.027	0.003	0.050
SnpSetSegments-class	0.004	0.001	0.004
backgroundCorrect.SNP	0.001	0.000	0.001
calculateQCarray	0.001	0.000	0.001
compareGenotypes	0.009	0.002	0.010
dist.GT	0.137	0.017	0.157
heterozygosity	0.038	0.002	0.049
heterozygousSNPs	0.108	0.002	0.115
normalizeBetweenAlleles.SNP	0.096	0.003	0.100
normalizeBetweenSubsamples.SNP	0.076	0.004	0.081
normalizeLoci.SNP	0.035	0.001	0.036
normalizeWithinArrays.SNP	0.035	0.002	0.037
pdfChromosomesSmoothCopyNumber	0.001	0.001	0.001
plotQC	0.009	0.001	0.010
read.SnpSetIllumina	1.672	0.016	1.694
removeLowQualitySamples	0.048	0.001	0.049
reportSamplePanelQC-methods	0.016	0.001	0.021
standardNormalization	0.159	0.003	0.162