Package: lumi

Version: 2.6.0

Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch lumi_2.6.0.tar.gz

StartedAt: 2012-01-09 03:58:37 -0800 (Mon, 09 Jan 2012)

EndedAt: 2012-01-09 04:07:19 -0800 (Mon, 09 Jan 2012)

EllapsedTime: 521.8 seconds

RetCode: 0

Status:  OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/lumi.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-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 '2.6.0'
* 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 'lumi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    8.4Mb
* 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 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: IlluminaID2nuID.Rd:28-29: Dropping empty section \examples
prepare_Rd: addAnnotationInfo.Rd:17-20: 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:31-33: 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:29-31: Dropping empty section \references
prepare_Rd: plotColorBias2D.Rd:32-34: 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:23-25: Dropping empty section \details
prepare_Rd: smoothQuantileNormalization.Rd:29-31: Dropping empty section \references
prepare_Rd: smoothQuantileNormalization.Rd:39-41: 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                             old_size new_size compress
  example.lumi.rda              940Kb    405Kb       xz
  example.lumiMethy.rda         1.1Mb    911Kb       xz
  example.methyTitration.rda    1.5Mb    1.1Mb       xz
* 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

* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'IlluminaAnnotation.Rnw' 
   'lumi.Rnw' 
   'lumi_VST_evaluation.Rnw' 
   'methylationAnalysis.Rnw' 
** testing if installed package can be loaded

* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	0.98	0.00	1.00
MAplot-methods	6.38	0.03	6.41
addAnnotationInfo	0.09	0.00	0.09
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	1.63	0.02	1.64
adjColorBias.ssn	1.09	0.00	1.11
bgAdjust	0.06	0.01	0.08
bgAdjustMethylation	0.60	0.00	0.59
boxplot-MethyLumiM-methods	3.04	0.10	3.16
boxplot-methods	0.22	0.00	0.22
boxplotColorBias	0.84	0.03	0.87
density-methods	0.11	0.00	0.11
detectOutlier	0.10	0.01	0.11
detectionCall	0.15	0.00	0.22
estimateBeta	0.22	0.00	0.28
estimateIntensity	0.33	0.00	0.33
estimateLumiCV	0.13	0.00	0.13
estimateM	2.15	0.10	2.25
estimateMethylationBG	0.24	0.00	0.23
example.lumi	0.07	0.00	0.08
example.lumiMethy	0.08	0.00	0.08
example.methyTitration	0.14	0.00	0.14
gammaFitEM	6.05	0.00	6.04
getChipInfo	6.02	0.29	10.24
getControlData	0.67	0.00	0.68
getControlProbe	0.18	0.00	0.17
getControlType	0.15	0.00	0.15
getNuIDMappingInfo	19.16	0.05	19.27
hist-methods	0.12	0.02	0.14
id2seq	0	0	0
inverseVST	0.73	0.00	0.75
is.nuID	0	0	0
lumiB	0.10	0.00	0.09
lumiExpresso	0.65	0.00	0.66
lumiMethyB	0.08	0.00	0.08
lumiMethyC	1.75	0.00	1.75
lumiMethyN	0.11	0.00	0.11
lumiMethyStatus	147.03	0.00	147.14
lumiN	0.86	0.00	0.89
lumiQ	0.36	0.01	0.38
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.57	0.00	0.57
methylationCall	9.44	0.00	9.44
normalizeMethylation.quantile	0.19	0.00	0.20
normalizeMethylation.ssn	0.34	0.00	0.35
nuID2EntrezID	17.05	0.03	17.08
nuID2IlluminaID	6.60	0.02	6.64
nuID2RefSeqID	15.13	0.03	15.16
nuID2probeID	7.14	0.02	7.16
nuID2targetID	6.32	0.00	6.33
pairs-methods	1.80	0.03	1.84
plot-methods	3.11	0.01	3.19
plotCDF	0.25	0.00	0.25
plotColorBias1D	0.42	0.00	0.42
plotColorBias2D	0.31	0.00	0.31
plotControlData	0.21	0.00	0.21
plotDensity	0.22	0.00	0.22
plotGammaFit	8.82	0.00	8.82
plotHousekeepingGene	0.21	0.00	0.21
plotSampleRelation	1.01	0.00	1.01
plotStringencyGene	0.21	0.00	0.21
plotVST	0.56	0.00	0.62
probeID2nuID	6.50	0.06	6.56
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	7.80	0.03	7.83
vst	0.81	0.00	0.82