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Package 232/419HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 2.2.1
Pan Du
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/lumi
Last Changed Rev: 51657 / Revision: 54281
Last Changed Date: 2010-12-21 12:47:03 -0800 (Tue, 21 Dec 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: lumi
Version: 2.2.1
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings lumi_2.2.1.tar.gz
StartedAt: 2011-03-31 07:09:42 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 07:14:39 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 297.4 seconds
RetCode: 0
Status:  OK  
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/lumi.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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

lumi.Rcheck/00install.out:

* 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)

lumi.Rcheck/lumi-Ex.timings:

nameusersystemelapsed
LumiBatch-class0.980.021.00
MAplot-methods10.08 0.0310.11
MethyLumiM-class000
addColorChannelInfo0.120.010.14
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile4.250.004.25
adjColorBias.ssn4.170.004.17
bgAdjust0.10.00.1
bgAdjustMethylation1.310.021.33
boxplot-MethyLumiM-methods3.950.144.09
boxplot-methods0.330.000.33
boxplotColorBias1.810.051.87
density-methods0.180.000.17
detectOutlier0.120.000.13
detectionCall0.240.000.23
estimateBeta0.430.000.46
estimateIntensity0.430.000.43
estimateLumiCV0.180.000.19
estimateM3.420.093.52
estimateMethylationBG1.240.001.23
example.lumi0.090.000.10
example.lumiMethy0.130.000.14
example.methyTitration0.190.000.22
getChipInfo5.400.176.73
getControlData0.80.00.8
getControlProbe0.280.000.28
getControlType0.340.000.34
getNuIDMappingInfo14.19 0.0214.30
hist-methods0.160.000.15
id2seq0.010.000.02
inverseVST0.580.000.59
is.nuID000
lumiB0.110.000.11
lumiExpresso0.720.000.72
lumiMethyB0.110.000.11
lumiMethyC4.800.034.83
lumiMethyN0.160.000.15
lumiN2.330.002.35
lumiQ0.670.010.68
lumiR000
lumiR.batch000
lumiT1.480.021.50
normalizeMethylation.quantile0.270.000.27
normalizeMethylation.ssn1.260.001.26
nuID2EntrezID10.16 0.0010.16
nuID2IlluminaID7.430.037.46
nuID2RefSeqID14.47 0.0014.50
nuID2probeID7.250.007.25
nuID2targetID7.130.007.14
pairs-methods4.610.004.63
plot-methods3.730.033.78
plotCDF0.800.000.79
plotColorBias1D1.50.01.5
plotColorBias2D0.390.000.39
plotControlData0.280.000.29
plotDensity0.260.000.26
plotHousekeepingGene0.290.000.30
plotSampleRelation1.730.001.73
plotStringencyGene0.270.000.27
plotVST1.620.001.62
probeID2nuID6.800.036.85
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID6.360.036.44
vst0.880.040.91