BioC 2.7: CHECK report for lumi on pelham

Package: lumi

Version: 2.2.1

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.2.1.tar.gz

StartedAt: 2011-03-31 06:33:07 -0700 (Thu, 31 Mar 2011)

EndedAt: 2011-03-31 06:39:00 -0700 (Thu, 31 Mar 2011)

EllapsedTime: 352.7 seconds

RetCode: 0

Status: OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/lumi.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-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 ‘2.2.1’
* 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: 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:25-26: 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: 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:30-32: 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: 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:26: 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
  'openVignette()'. 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	1.237	0.054	1.303
MAplot-methods	9.110	0.390	9.633
MethyLumiM-class	0.003	0.000	0.003
addColorChannelInfo	0.151	0.007	0.161
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0	0	0
adjColorBias.quantile	1.429	0.216	1.667
adjColorBias.ssn	1.252	0.189	1.476
bgAdjust	0.141	0.008	0.151
bgAdjustMethylation	0.608	0.095	0.711
boxplot-MethyLumiM-methods	3.031	0.246	3.335
boxplot-methods	0.357	0.024	0.384
boxplotColorBias	0.917	0.142	1.074
density-methods	0.159	0.013	0.175
detectOutlier	0.170	0.030	0.204
detectionCall	0.269	0.021	0.299
estimateBeta	0.371	0.044	0.419
estimateIntensity	0.501	0.057	0.568
estimateLumiCV	0.163	0.014	0.178
estimateM	2.351	0.257	2.634
estimateMethylationBG	0.394	0.057	0.464
example.lumi	0.138	0.006	0.146
example.lumiMethy	0.148	0.007	0.155
example.methyTitration	0.249	0.011	0.262
getChipInfo	6.296	0.790	7.461
getControlData	0.947	0.043	0.999
getControlProbe	0.212	0.006	0.219
getControlType	0.272	0.011	0.285
getNuIDMappingInfo	21.775	0.240	22.931
hist-methods	0.164	0.014	0.179
id2seq	0.002	0.000	0.002
inverseVST	0.695	0.105	0.830
is.nuID	0.001	0.000	0.001
lumiB	0.192	0.012	0.206
lumiExpresso	0.638	0.081	0.731
lumiMethyB	0.148	0.005	0.154
lumiMethyC	1.759	0.229	2.278
lumiMethyN	0.240	0.015	0.298
lumiN	1.533	0.145	1.717
lumiQ	0.380	0.064	0.449
lumiR	0.000	0.000	0.001
lumiR.batch	0.000	0.001	0.001
lumiT	0.577	0.086	0.671
normalizeMethylation.quantile	0.324	0.036	0.384
normalizeMethylation.ssn	0.527	0.082	0.641
nuID2EntrezID	15.519	0.120	16.068
nuID2IlluminaID	6.197	0.300	6.570
nuID2RefSeqID	27.260	0.168	28.528
nuID2probeID	6.610	0.314	7.047
nuID2targetID	6.543	0.307	6.996
pairs-methods	1.912	0.250	2.222
plot-methods	4.377	0.208	4.636
plotCDF	0.266	0.028	0.295
plotColorBias1D	0.415	0.056	0.479
plotColorBias2D	0.210	0.015	0.229
plotControlData	0.346	0.010	0.357
plotDensity	0.182	0.012	0.194
plotHousekeepingGene	0.368	0.009	0.387
plotSampleRelation	2.165	0.032	2.216
plotStringencyGene	0.335	0.007	0.392
plotVST	0.661	0.088	0.789
probeID2nuID	7.206	0.298	7.638
produceGEOPlatformFile	0.000	0.000	0.001
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	7.353	0.297	7.713
vst	1.275	0.100	1.389

Summary

Command output