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: 2011-03-17 16:45:02 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 16:51:12 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 370.3 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) (2011-03-06 r54683)
* 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 installed package size ... NOTE
  installed size is 32.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc   28.8Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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	0.804	0.010	0.815
MAplot-methods	6.425	0.048	6.473
addColorChannelInfo	0.103	0.002	0.104
addControlData2lumi	0	0	0
addNuID2lumi	0.000	0.001	0.000
adjColorBias.quantile	0.951	0.009	0.960
adjColorBias.ssn	0.967	0.016	0.982
bgAdjust	0.096	0.003	0.098
bgAdjustMethylation	0.438	0.007	0.445
boxplot-MethyLumiM-methods	2.257	0.087	2.345
boxplot-methods	0.253	0.004	0.256
boxplotColorBias	0.636	0.035	0.672
density-methods	0.107	0.004	0.111
detectOutlier	0.110	0.009	0.119
detectionCall	0.165	0.003	0.168
estimateBeta	0.250	0.011	0.259
estimateIntensity	0.339	0.009	0.348
estimateLumiCV	0.105	0.003	0.108
estimateM	1.704	0.084	1.789
estimateMethylationBG	0.270	0.002	0.271
example.lumi	0.093	0.002	0.095
example.lumiMethy	0.101	0.003	0.104
example.methyTitration	0.171	0.003	0.174
gammaFitEM	5.221	0.903	6.124
getChipInfo	4.217	0.317	4.855
getControlData	0.861	0.016	0.877
getControlProbe	0.209	0.004	0.212
getControlType	0.192	0.002	0.195
getNuIDMappingInfo	8.514	0.112	8.653
hist-methods	0.137	0.005	0.142
id2seq	0.001	0.001	0.001
inverseVST	0.485	0.030	0.516
is.nuID	0.001	0.000	0.001
lumiB	0.093	0.001	0.095
lumiExpresso	0.378	0.018	0.396
lumiMethyB	0.099	0.002	0.101
lumiMethyC	1.097	0.050	1.148
lumiMethyN	0.140	0.003	0.142
lumiMethyStatus	114.377	6.903	121.285
lumiN	0.876	0.023	0.899
lumiQ	0.277	0.010	0.287
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.437	0.007	0.443
methylationCall	7.239	0.883	8.122
normalizeMethylation.quantile	0.199	0.012	0.211
normalizeMethylation.ssn	0.358	0.018	0.376
nuID2EntrezID	6.937	0.034	6.971
nuID2IlluminaID	5.089	0.087	5.176
nuID2RefSeqID	9.159	0.034	9.193
nuID2probeID	4.204	0.087	4.291
nuID2targetID	4.385	0.086	4.472
pairs-methods	1.460	0.065	1.525
plot-methods	2.529	0.036	2.566
plotCDF	0.182	0.009	0.191
plotColorBias1D	0.388	0.016	0.404
plotColorBias2D	0.130	0.007	0.137
plotControlData	0.214	0.005	0.218
plotDensity	0.104	0.003	0.106
plotGammaFit	7.183	0.734	7.917
plotHousekeepingGene	0.214	0.003	0.217
plotSampleRelation	1.618	0.010	1.628
plotStringencyGene	0.222	0.002	0.226
plotVST	0.459	0.014	0.544
probeID2nuID	5.600	0.091	5.692
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.000	0.001	0.000
targetID2nuID	5.215	0.093	5.308
vst	0.583	0.029	0.612