Package: lumi

Version: 2.6.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.6.0.tar.gz

StartedAt: 2012-03-24 02:11:43 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 02:26:07 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 864.4 seconds

RetCode: 0

Status:  OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/lumi.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '2.6.0'
* 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 11.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    7.7Mb
* 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 ... 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    903Kb       xz
  example.methyTitration.rda    1.5Mb    1.1Mb       xz
* checking sizes of PDF files under 'inst/doc' ... OK
* 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	1.340	0.052	1.407
MAplot-methods	9.213	0.361	9.644
addAnnotationInfo	0.157	0.007	0.166
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	2.253	0.276	2.566
adjColorBias.ssn	1.577	0.175	1.772
bgAdjust	0.143	0.008	0.151
bgAdjustMethylation	0.925	0.085	1.011
boxplot-MethyLumiM-methods	3.778	0.241	4.184
boxplot-methods	0.329	0.023	0.360
boxplotColorBias	0.952	0.134	1.099
density-methods	0.163	0.014	0.184
detectOutlier	0.184	0.034	0.219
detectionCall	0.270	0.014	0.285
estimateBeta	0.357	0.044	0.406
estimateIntensity	0.504	0.055	0.562
estimateLumiCV	0.408	0.025	0.444
estimateM	2.742	0.230	3.011
estimateMethylationBG	0.375	0.052	0.427
example.lumi	0.138	0.006	0.148
example.lumiMethy	0.153	0.007	0.161
example.methyTitration	0.254	0.011	0.266
gammaFitEM	8.659	6.585	15.370
getChipInfo	6.821	0.806	8.130
getControlData	0.682	0.061	0.748
getControlProbe	0.229	0.008	0.240
getControlType	0.170	0.006	0.197
getNuIDMappingInfo	34.163	0.171	35.325
hist-methods	0.294	0.016	0.312
id2seq	0.001	0.001	0.002
inverseVST	0.853	0.096	1.009
is.nuID	0.001	0.000	0.001
lumiB	0.147	0.007	0.155
lumiExpresso	0.745	0.079	0.846
lumiMethyB	0.152	0.006	0.158
lumiMethyC	2.853	0.254	3.149
lumiMethyN	0.197	0.012	0.209
lumiMethyStatus	188.435	132.358	335.867
lumiN	1.154	0.170	1.387
lumiQ	0.534	0.084	0.625
lumiR	0.000	0.001	0.001
lumiR.batch	0	0	0
lumiT	0.829	0.126	0.970
methylationCall	11.353	7.626	19.555
normalizeMethylation.quantile	0.283	0.040	0.327
normalizeMethylation.ssn	0.790	0.102	0.910
nuID2EntrezID	23.220	0.111	23.470
nuID2IlluminaID	7.274	0.352	7.712
nuID2RefSeqID	25.372	0.124	25.756
nuID2probeID	7.421	0.339	7.803
nuID2targetID	6.799	0.352	7.230
pairs-methods	2.562	0.281	2.889
plot-methods	4.865	0.271	5.196
plotCDF	0.756	0.039	0.910
plotColorBias1D	0.536	0.072	0.611
plotColorBias2D	0.346	0.021	0.367
plotControlData	0.359	0.018	0.377
plotDensity	0.197	0.014	0.212
plotGammaFit	11.767	7.512	19.785
plotHousekeepingGene	0.366	0.013	0.388
plotSampleRelation	1.515	0.035	1.620
plotStringencyGene	0.310	0.008	0.319
plotVST	0.772	0.113	0.899
probeID2nuID	7.457	0.356	7.988
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0.001	0.000	0.000
produceMethylationGEOSubmissionFile	0.000	0.001	0.000
seq2id	0.001	0.000	0.001
targetID2nuID	7.336	0.340	7.741
vst	0.871	0.118	1.005