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Package 50/467HostnameOS / ArchBUILDCHECKBUILD BIN
beadarraySNP 1.18.0
Jan Oosting
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/beadarraySNP
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 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 SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: beadarraySNP
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch beadarraySNP_1.18.0.tar.gz
StartedAt: 2011-10-20 13:37:06 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 13:39:09 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 122.9 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 2.13.2 (2011-09-30)
* 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 '1.18.0'
* checking package namespace 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 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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'beadarraySNP.pdf' from 502Kb to 212Kb
  consider running tools::compactPDF() on these files
* 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
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (beadarraySNP)

beadarraySNP.Rcheck/beadarraySNP-Ex.timings:

nameusersystemelapsed
GenomicReports 5.833 0.67411.363
PolarTransforms0.0260.0040.048
SnpSetSegments-class0.0020.0010.002
backgroundCorrect.SNP000
calculateQCarray000
compareGenotypes0.0120.0020.022
dist.GT0.1240.0030.205
heterozygosity0.0550.0040.081
heterozygousSNPs0.1400.0040.241
normalizeBetweenAlleles.SNP0.0980.0110.152
normalizeBetweenSubsamples.SNP0.0730.0050.141
normalizeLoci.SNP0.0430.0050.084
normalizeWithinArrays.SNP0.0500.0040.077
pdfChromosomesSmoothCopyNumber000
plotQC0.0080.0010.018
read.SnpSetIllumina1.0220.0201.876
removeLowQualitySamples0.0610.0040.077
reportSamplePanelQC-methods0.0150.0010.038
standardNormalization0.1870.0110.396