BioC 2.8: CHECK report for lumi on liverpool

Package: lumi

Version: 2.3.7

Command: E:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings lumi_2.3.7.tar.gz

StartedAt: 2011-02-24 18:40:07 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 18:46:34 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 386.8 seconds

RetCode: 0

Status: OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.8-bioc/meat/lumi.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.3.7'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'lumi' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: IlluminaID2nuID.Rd:28-29: Dropping empty section \examples
prepare_Rd: addColorChannelInfo.Rd:15-17: Dropping empty section \details
prepare_Rd: addControlData2lumi.Rd:22: Dropping empty section \references
prepare_Rd: addControlData2methyLumiM.Rd:30-32: Dropping empty section \examples
prepare_Rd: adjColorBias.quantile.Rd:28-30: Dropping empty section \references
prepare_Rd: adjColorBias.ssn.Rd:26-27: Dropping empty section \references
prepare_Rd: beta2m.Rd:39-41: Dropping empty section \examples
prepare_Rd: bgAdjustMethylation.Rd:26-28: Dropping empty section \references
prepare_Rd: boxplotColorBias.Rd:30-32: Dropping empty section \references
prepare_Rd: colorBiasSummary.Rd:29-31: Dropping empty section \examples
prepare_Rd: estimateBeta.Rd:27-29: Dropping empty section \references
prepare_Rd: estimateIntensity.Rd:24-26: Dropping empty section \references
prepare_Rd: estimateMethylationBG.Rd:27-28: Dropping empty section \references
prepare_Rd: example.lumiMethy.Rd:16-18: Dropping empty section \references
prepare_Rd: example.methyTitration.Rd:16-18: Dropping empty section \references
prepare_Rd: gammaFitEM.Rd:40-42: Dropping empty section \references
prepare_Rd: getChipInfo.Rd:34: Dropping empty section \references
prepare_Rd: getControlData.Rd:17-19: Dropping empty section \details
prepare_Rd: getControlData.Rd:23: Dropping empty section \references
prepare_Rd: getControlProbe.Rd:16-18: Dropping empty section \details
prepare_Rd: getControlProbe.Rd:22: Dropping empty section \references
prepare_Rd: getControlType.Rd:15-17: Dropping empty section \details
prepare_Rd: getControlType.Rd:21: Dropping empty section \references
prepare_Rd: lumi.package.Rd:35-37: Dropping empty section \seealso
prepare_Rd: lumi.package.Rd:38-40: Dropping empty section \examples
prepare_Rd: lumiMethyB.Rd:21-23: Dropping empty section \details
prepare_Rd: lumiMethyB.Rd:27-29: Dropping empty section \references
prepare_Rd: lumiMethyC.Rd:26-28: Dropping empty section \references
prepare_Rd: lumiMethyN.Rd:21-23: Dropping empty section \details
prepare_Rd: lumiMethyN.Rd:27-29: Dropping empty section \references
prepare_Rd: lumiMethyR.Rd:31-33: Dropping empty section \examples
prepare_Rd: lumiN.Rd:28-30: Dropping empty section \note
prepare_Rd: lumiN.Rd:26: Dropping empty section \references
prepare_Rd: m2beta.Rd:37-39: Dropping empty section \examples
prepare_Rd: methylationCall.Rd:25-27: Dropping empty section \references
prepare_Rd: monoSmu.Rd:36-38: Dropping empty section \examples
prepare_Rd: monoSpline.Rd:25: Dropping empty section \references
prepare_Rd: monoSpline.Rd:29-31: Dropping empty section \examples
prepare_Rd: normalizeMethylation.quantile.Rd:19-21: Dropping empty section \details
prepare_Rd: normalizeMethylation.quantile.Rd:25-27: Dropping empty section \references
prepare_Rd: normalizeMethylation.ssn.Rd:18-20: Dropping empty section \details
prepare_Rd: normalizeMethylation.ssn.Rd:24-26: Dropping empty section \references
prepare_Rd: plotColorBias1D.Rd:28-30: Dropping empty section \references
prepare_Rd: plotColorBias2D.Rd:31-33: Dropping empty section \references
prepare_Rd: plotControlData.Rd:27: Dropping empty section \references
prepare_Rd: plotGammaFit.Rd:31-33: Dropping empty section \references
prepare_Rd: plotHousekeepingGene.Rd:20-22: Dropping empty section \details
prepare_Rd: plotHousekeepingGene.Rd:26: Dropping empty section \references
prepare_Rd: plotStringencyGene.Rd:20-22: Dropping empty section \details
prepare_Rd: plotStringencyGene.Rd:26: Dropping empty section \references
prepare_Rd: plotVST.Rd:19-22: Dropping empty section \details
prepare_Rd: produceGEOSampleInfoTemplate.Rd:27-29: Dropping empty section \examples
prepare_Rd: rankinvariant.Rd:29: Dropping empty section \references
prepare_Rd: rankinvariant.Rd:32-34: Dropping empty section \examples
prepare_Rd: rsn.Rd:33-35: Dropping empty section \note
prepare_Rd: rsn.Rd:29-31: Dropping empty section \references
prepare_Rd: rsn.Rd:37-39: Dropping empty section \examples
prepare_Rd: smoothQuantileNormalization.Rd:22-24: Dropping empty section \details
prepare_Rd: smoothQuantileNormalization.Rd:28-30: Dropping empty section \references
prepare_Rd: smoothQuantileNormalization.Rd:38-40: Dropping empty section \examples
prepare_Rd: ssn.Rd:28: Dropping empty section \references
prepare_Rd: ssn.Rd:31-33: Dropping empty section \examples
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'lumi' ...
** 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)'.

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Creating a new generic function for "summary" in "lumi"
Creating a new generic function for "boxplot" in "lumi"
Creating a new generic function for "hist" in "lumi"
Creating a new generic function for "density" in "lumi"
Creating a new generic function for "pairs" in "lumi"
Creating a new generic function for "plot" in "lumi"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	0.79	0.00	0.79
MAplot-methods	6.91	0.00	6.90
addColorChannelInfo	0.11	0.00	0.11
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	1.09	0.01	1.11
adjColorBias.ssn	1.14	0.00	1.14
bgAdjust	0.09	0.00	0.10
bgAdjustMethylation	0.52	0.00	0.51
boxplot-MethyLumiM-methods	2.52	0.05	2.57
boxplot-methods	0.25	0.02	0.26
boxplotColorBias	0.78	0.00	0.78
density-methods	0.12	0.00	0.13
detectOutlier	0.10	0.01	0.11
detectionCall	0.18	0.02	0.20
estimateBeta	0.27	0.01	0.28
estimateIntensity	0.40	0.00	0.41
estimateLumiCV	0.13	0.00	0.12
estimateM	1.81	0.02	1.83
estimateMethylationBG	0.28	0.00	0.28
example.lumi	0.11	0.00	0.11
example.lumiMethy	0.11	0.00	0.11
example.methyTitration	0.19	0.00	0.18
gammaFitEM	5.75	0.05	5.80
getChipInfo	5.51	0.21	7.25
getControlData	0.78	0.00	0.78
getControlProbe	0.19	0.00	0.21
getControlType	0.25	0.02	0.26
getNuIDMappingInfo	12.67	0.05	13.09
hist-methods	0.12	0.00	0.13
id2seq	0	0	0
inverseVST	0.47	0.01	0.51
is.nuID	0	0	0
lumiB	0.11	0.00	0.11
lumiExpresso	0.50	0.02	0.51
lumiMethyB	0.11	0.00	0.11
lumiMethyC	1.27	0.00	1.27
lumiMethyN	0.2	0.0	0.2
lumiMethyStatus	114.86	0.01	115.00
lumiN	1.11	0.00	1.12
lumiQ	0.64	0.00	0.65
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.58	0.00	0.57
methylationCall	8.48	0.00	8.49
normalizeMethylation.quantile	0.25	0.00	0.25
normalizeMethylation.ssn	0.36	0.00	0.36
nuID2EntrezID	11.86	0.00	11.86
nuID2IlluminaID	7.55	0.00	7.54
nuID2RefSeqID	14.64	0.04	14.68
nuID2probeID	6.92	0.00	6.92
nuID2targetID	6.89	0.01	6.90
pairs-methods	2.72	0.00	2.74
plot-methods	2.92	0.03	2.95
plotCDF	0.25	0.00	0.25
plotColorBias1D	0.36	0.02	0.38
plotColorBias2D	0.20	0.01	0.21
plotControlData	0.24	0.00	0.24
plotDensity	0.15	0.00	0.16
plotGammaFit	7.99	0.00	7.98
plotHousekeepingGene	0.39	0.02	0.41
plotSampleRelation	1.4	0.0	1.4
plotStringencyGene	0.24	0.00	0.24
plotVST	0.7	0.0	0.7
probeID2nuID	7.80	0.00	7.81
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	6.78	0.03	6.81
vst	0.68	0.00	0.67

Summary

Command output