Package: beadarraySNP

Version: 1.22.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings beadarraySNP_1.22.0.tar.gz

StartedAt: 2012-09-23 23:31:01 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 23:32:10 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 68.9 seconds

RetCode: 0

Status:  OK

CheckDir: beadarraySNP.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/beadarraySNP.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.22.0’
* 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 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 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 installed files from ‘inst/doc’ ... 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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-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	3.804	0.052	4.024
PolarTransforms	0.020	0.000	0.022
SnpSetSegments-class	0.004	0.000	0.001
backgroundCorrect.SNP	0	0	0
calculateQCarray	0	0	0
compareGenotypes	0.004	0.000	0.006
dist.GT	0.084	0.008	0.089
heterozygosity	0.028	0.004	0.032
heterozygousSNPs	0.084	0.004	0.088
normalizeBetweenAlleles.SNP	0.056	0.000	0.054
normalizeBetweenSubsamples.SNP	0.032	0.004	0.040
normalizeLoci.SNP	0.02	0.00	0.03
normalizeWithinArrays.SNP	0.024	0.000	0.028
pdfChromosomesSmoothCopyNumber	0	0	0
plotQC	0.008	0.000	0.007
read.SnpSetIllumina	1.140	0.008	1.165
removeLowQualitySamples	0.04	0.00	0.04
reportSamplePanelQC-methods	0.012	0.000	0.011
standardNormalization	0.096	0.000	0.094