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Package 259/462HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 2.5.1
Pan Du
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi
Last Changed Rev: 55052 / Revision: 55359
Last Changed Date: 2011-04-23 17:59:02 -0700 (Sat, 23 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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: 2.5.1
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings lumi_2.5.1.tar.gz
StartedAt: 2011-05-09 14:21:49 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:28:54 -0700 (Mon, 09 May 2011)
EllapsedTime: 425.7 seconds
RetCode: 0
Status:  OK  
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/lumi.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '2.5.1'
* 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 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 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: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 ... 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

lumi.Rcheck/00install.out:

* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

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
** 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)

lumi.Rcheck/lumi-Ex.timings:

nameusersystemelapsed
LumiBatch-class0.820.000.82
MAplot-methods6.930.057.00
addColorChannelInfo0.250.000.25
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile2.220.002.23
adjColorBias.ssn1.30.01.3
bgAdjust0.090.000.09
bgAdjustMethylation0.640.000.64
boxplot-MethyLumiM-methods2.410.032.44
boxplot-methods0.280.000.28
boxplotColorBias0.780.000.78
density-methods0.130.000.13
detectOutlier0.120.000.12
detectionCall0.190.000.19
estimateBeta0.290.000.28
estimateIntensity0.390.000.39
estimateLumiCV0.150.000.15
estimateM1.910.061.97
estimateMethylationBG0.310.000.31
example.lumi0.10.00.1
example.lumiMethy0.120.000.12
example.methyTitration0.200.000.21
gammaFitEM5.800.005.82
getChipInfo5.630.087.10
getControlData0.890.030.92
getControlProbe0.20.00.2
getControlType0.220.000.22
getNuIDMappingInfo10.20 0.0110.30
hist-methods0.130.000.12
id2seq000
inverseVST0.490.000.52
is.nuID000
lumiB0.110.000.10
lumiExpresso0.560.000.57
lumiMethyB0.140.020.15
lumiMethyC2.780.002.78
lumiMethyN0.410.000.41
lumiMethyStatus120.36 0.00120.84
lumiN1.250.001.27
lumiQ0.390.020.41
lumiR000
lumiR.batch000
lumiT0.620.010.64
methylationCall8.990.009.00
normalizeMethylation.quantile0.240.000.24
normalizeMethylation.ssn0.40.00.4
nuID2EntrezID13.29 0.0013.31
nuID2IlluminaID8.460.008.63
nuID2RefSeqID15.58 0.0015.72
nuID2probeID7.730.007.81
nuID2targetID6.950.007.00
pairs-methods2.720.062.83
plot-methods2.920.023.07
plotCDF0.280.000.29
plotColorBias1D0.410.000.40
plotColorBias2D0.270.000.27
plotControlData0.290.000.29
plotDensity0.180.020.19
plotGammaFit8.310.008.31
plotHousekeepingGene0.250.000.30
plotSampleRelation1.400.001.41
plotStringencyGene0.220.010.23
plotVST0.670.000.69
probeID2nuID7.330.007.36
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID6.780.026.84
vst1.070.001.06