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Package 50/462HostnameOS / ArchBUILDCHECKBUILD BIN
beadarraySNP 1.19.0
Jan Oosting
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarraySNP
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 

Summary

Package: beadarraySNP
Version: 1.19.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings beadarraySNP_1.19.0.tar.gz
StartedAt: 2011-05-09 11:35:55 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 11:36:52 -0700 (Mon, 09 May 2011)
EllapsedTime: 57.8 seconds
RetCode: 0
Status:  OK 
CheckDir: beadarraySNP.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/beadarraySNP.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* 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 ‘1.19.0’
* 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 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

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 (0.89) 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 ...
*** tangling vignette sources ...
   ‘beadarraySNP.rnw’ 
** testing if installed package can be loaded

* DONE (beadarraySNP)

beadarraySNP.Rcheck/beadarraySNP-Ex.timings:

nameusersystemelapsed
GenomicReports4.8160.0724.897
PolarTransforms0.0120.0040.018
SnpSetSegments-class0.0040.0000.002
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes0.0040.0000.007
dist.GT0.0720.0160.091
heterozygosity0.0320.0000.032
heterozygousSNPs0.0920.0000.093
normalizeBetweenAlleles.SNP0.0480.0160.061
normalizeBetweenSubsamples.SNP0.0360.0000.037
normalizeLoci.SNP0.0280.0000.031
normalizeWithinArrays.SNP0.0360.0000.035
pdfChromosomesSmoothCopyNumber000
plotQC0.0080.0000.006
read.SnpSetIllumina1.0920.0001.090
removeLowQualitySamples0.0440.0000.045
reportSamplePanelQC-methods0.0080.0040.011
standardNormalization0.1080.0080.119