BioC 2.8: CHECK report for lumi on petty

Package: lumi

Version: 2.3.7

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.3.7.tar.gz

StartedAt: 2011-02-24 16:06:16 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 16:11:58 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 341.7 seconds

RetCode: 0

Status: OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/lumi.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 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 ... 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	0.771	0.010	0.781
MAplot-methods	6.359	0.055	6.414
addColorChannelInfo	0.098	0.002	0.100
addControlData2lumi	0.000	0.001	0.001
addNuID2lumi	0.001	0.000	0.000
adjColorBias.quantile	0.797	0.010	0.806
adjColorBias.ssn	0.904	0.015	0.919
bgAdjust	0.087	0.002	0.089
bgAdjustMethylation	0.403	0.009	0.413
boxplot-MethyLumiM-methods	2.049	0.085	2.134
boxplot-methods	0.247	0.005	0.252
boxplotColorBias	0.619	0.036	0.656
density-methods	0.106	0.005	0.111
detectOutlier	0.112	0.010	0.122
detectionCall	0.170	0.003	0.173
estimateBeta	0.249	0.011	0.261
estimateIntensity	0.337	0.010	0.348
estimateLumiCV	0.109	0.004	0.112
estimateM	1.725	0.100	1.826
estimateMethylationBG	0.263	0.003	0.265
example.lumi	0.089	0.002	0.090
example.lumiMethy	0.095	0.002	0.096
example.methyTitration	0.160	0.003	0.164
gammaFitEM	5.072	0.917	5.990
getChipInfo	4.491	0.321	5.024
getControlData	0.715	0.021	0.737
getControlProbe	0.195	0.002	0.198
getControlType	0.234	0.007	0.242
getNuIDMappingInfo	10.778	0.095	10.884
hist-methods	0.102	0.005	0.108
id2seq	0.001	0.001	0.001
inverseVST	0.392	0.025	0.418
is.nuID	0.000	0.000	0.001
lumiB	0.126	0.002	0.127
lumiExpresso	0.426	0.016	0.442
lumiMethyB	0.099	0.003	0.102
lumiMethyC	1.009	0.052	1.061
lumiMethyN	0.155	0.005	0.159
lumiMethyStatus	103.292	13.982	117.278
lumiN	0.936	0.019	0.955
lumiQ	0.238	0.012	0.250
lumiR	0.001	0.001	0.001
lumiR.batch	0	0	0
lumiT	0.389	0.014	0.403
methylationCall	6.755	0.712	7.468
normalizeMethylation.quantile	0.199	0.011	0.210
normalizeMethylation.ssn	0.424	0.019	0.443
nuID2EntrezID	7.683	0.044	7.727
nuID2IlluminaID	4.566	0.097	4.663
nuID2RefSeqID	8.975	0.052	9.027
nuID2probeID	4.694	0.101	4.796
nuID2targetID	4.434	0.120	4.554
pairs-methods	1.184	0.089	1.272
plot-methods	2.611	0.043	2.653
plotCDF	0.172	0.004	0.176
plotColorBias1D	0.310	0.014	0.324
plotColorBias2D	0.136	0.003	0.140
plotControlData	0.226	0.010	0.319
plotDensity	0.119	0.005	0.125
plotGammaFit	6.460	0.847	7.308
plotHousekeepingGene	0.207	0.003	0.210
plotSampleRelation	1.565	0.006	1.572
plotStringencyGene	0.205	0.002	0.207
plotVST	0.541	0.022	0.584
probeID2nuID	4.655	0.084	4.739
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.000	0.000	0.001
targetID2nuID	4.529	0.084	4.614
vst	0.711	0.012	0.724

Summary

Command output