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Package 41/444HostnameOS / ArchBUILDCHECKBUILD BIN
beadarraySNP 1.17.0
Jan Oosting
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarraySNP
Last Changed Rev: 52658 / Revision: 53825
Last Changed Date: 2011-02-14 09:45:48 -0800 (Mon, 14 Feb 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ OK ] OK 

Summary

Package: beadarraySNP
Version: 1.17.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarraySNP_1.17.0.tar.gz
StartedAt: 2011-03-17 15:38:47 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 15:39:45 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 58.8 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/beadarraySNP.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'beadarraySNP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'beadarraySNP' version '1.17.0'
* 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 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 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 ... 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 examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

beadarraySNP.Rcheck/00install.out:

* installing *source* package 'beadarraySNP' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. 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)

beadarraySNP.Rcheck/beadarraySNP-Ex.timings:

nameusersystemelapsed
GenomicReports4.4490.1194.585
PolarTransforms0.0170.0010.018
SnpSetSegments-class0.0010.0000.002
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes0.0080.0010.009
dist.GT0.0930.0030.097
heterozygosity0.0380.0000.039
heterozygousSNPs0.1030.0010.104
normalizeBetweenAlleles.SNP0.0730.0040.078
normalizeBetweenSubsamples.SNP0.0500.0010.051
normalizeLoci.SNP0.0330.0010.034
normalizeWithinArrays.SNP0.0370.0010.037
pdfChromosomesSmoothCopyNumber0.0000.0000.001
plotQC0.0050.0010.006
read.SnpSetIllumina0.8740.0050.880
removeLowQualitySamples0.0450.0010.045
reportSamplePanelQC-methods0.0110.0000.011
standardNormalization0.1450.0030.146