Package: lumi

Version: 2.6.0

Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.6.0.tar.gz

StartedAt: 2012-03-24 01:16:01 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:25:42 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 581.4 seconds

RetCode: 0

Status:  OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/lumi.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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	1.520	0.008	1.529
MAplot-methods	6.060	0.056	6.123
addAnnotationInfo	0.072	0.000	0.070
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0	0	0
adjColorBias.quantile	1.973	0.020	1.992
adjColorBias.ssn	1.188	0.016	1.203
bgAdjust	0.068	0.004	0.071
bgAdjustMethylation	0.616	0.004	0.621
boxplot-MethyLumiM-methods	4.248	0.044	4.296
boxplot-methods	0.192	0.004	0.196
boxplotColorBias	0.796	0.000	0.798
density-methods	0.088	0.000	0.089
detectOutlier	0.104	0.004	0.106
detectionCall	0.136	0.000	0.133
estimateBeta	0.24	0.00	0.24
estimateIntensity	0.300	0.008	0.307
estimateLumiCV	0.100	0.004	0.104
estimateM	2.440	0.032	2.472
estimateMethylationBG	0.248	0.000	0.248
example.lumi	0.060	0.008	0.069
example.lumiMethy	0.068	0.000	0.067
example.methyTitration	0.112	0.004	0.119
gammaFitEM	7.293	0.016	7.312
getChipInfo	6.696	0.252	7.599
getControlData	0.524	0.020	0.545
getControlProbe	0.128	0.004	0.130
getControlType	0.124	0.000	0.124
getNuIDMappingInfo	30.366	0.052	31.035
hist-methods	0.792	0.004	0.797
id2seq	0.004	0.000	0.001
inverseVST	0.376	0.036	0.412
is.nuID	0.004	0.000	0.001
lumiB	0.1	0.0	0.1
lumiExpresso	0.344	0.000	0.343
lumiMethyB	0.060	0.008	0.068
lumiMethyC	1.596	0.008	1.608
lumiMethyN	0.100	0.004	0.103
lumiMethyStatus	158.150	0.048	160.021
lumiN	0.736	0.004	0.774
lumiQ	0.328	0.004	0.335
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.480	0.004	0.481
methylationCall	8.729	0.004	8.774
normalizeMethylation.quantile	0.156	0.000	0.158
normalizeMethylation.ssn	0.324	0.000	0.355
nuID2EntrezID	21.137	0.020	21.392
nuID2IlluminaID	6.925	0.028	6.981
nuID2RefSeqID	35.062	0.008	35.461
nuID2probeID	6.320	0.016	6.379
nuID2targetID	6.473	0.008	6.559
pairs-methods	1.208	0.024	1.236
plot-methods	3.060	0.016	3.077
plotCDF	0.240	0.000	0.239
plotColorBias1D	0.492	0.004	0.527
plotColorBias2D	0.228	0.000	0.229
plotControlData	0.208	0.000	0.208
plotDensity	0.200	0.004	0.207
plotGammaFit	15.813	0.000	15.970
plotHousekeepingGene	0.224	0.000	0.226
plotSampleRelation	0.984	0.004	0.999
plotStringencyGene	0.208	0.004	0.214
plotVST	0.448	0.000	0.447
probeID2nuID	6.648	0.032	6.734
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.004	0.000	0.000
targetID2nuID	6.353	0.020	6.443
vst	1.040	0.012	1.054