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Package 238/436HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 2.3.7
Pan Du
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi
Last Changed Rev: 52033 / Revision: 53255
Last Changed Date: 2011-01-23 18:38:10 -0800 (Sun, 23 Jan 2011)
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 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: lumi
Version: 2.3.7
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.3.7.tar.gz
StartedAt: 2011-02-24 20:40:58 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 20:47:25 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 387.0 seconds
RetCode: 0
Status:  OK 
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/lumi.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* 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 ‘2.3.7’
* 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: 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: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: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:28-30: Dropping empty section \references
prepare_Rd: plotColorBias2D.Rd:31-33: 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: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
  'browseVignettes()'. 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-class1.1280.0121.138
MAplot-methods6.4240.0206.454
addColorChannelInfo0.0600.0000.063
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile0.8960.0000.897
adjColorBias.ssn1.0840.0041.087
bgAdjust0.0640.0040.068
bgAdjustMethylation0.4680.0000.469
boxplot-MethyLumiM-methods2.9570.0723.038
boxplot-methods0.2080.0000.209
boxplotColorBias0.6400.0080.652
density-methods0.0800.0000.081
detectOutlier0.0920.0000.091
detectionCall0.1160.0000.118
estimateBeta0.2040.0000.204
estimateIntensity0.2720.0080.281
estimateLumiCV0.0840.0000.087
estimateM2.5320.0362.569
estimateMethylationBG0.2320.0000.233
example.lumi0.0640.0000.062
example.lumiMethy0.0640.0000.062
example.methyTitration0.1040.0040.109
gammaFitEM6.0840.0086.089
getChipInfo4.7810.1325.561
getControlData0.6160.0040.620
getControlProbe0.1280.0000.130
getControlType0.1760.0040.181
getNuIDMappingInfo21.073 0.02421.128
hist-methods0.0760.0080.083
id2seq0.0000.0000.001
inverseVST0.4160.0000.423
is.nuID0.0000.0000.001
lumiB0.0720.0000.070
lumiExpresso0.4200.0000.448
lumiMethyB0.0640.0000.062
lumiMethyC0.9600.0040.962
lumiMethyN0.0680.0080.091
lumiMethyStatus121.220 0.236121.573
lumiN1.0000.0081.029
lumiQ0.2240.0080.233
lumiR000
lumiR.batch000
lumiT0.3840.0080.391
methylationCall8.1760.0048.188
normalizeMethylation.quantile0.1520.0000.151
normalizeMethylation.ssn0.2960.0000.295
nuID2EntrezID16.281 0.00416.282
nuID2IlluminaID8.2170.0088.227
nuID2RefSeqID17.485 0.02417.517
nuID2probeID6.7320.0046.746
nuID2targetID6.9010.0166.930
pairs-methods1.3240.0121.342
plot-methods2.3280.0082.338
plotCDF0.1360.0000.140
plotColorBias1D0.2480.0000.250
plotColorBias2D0.0920.0000.093
plotControlData0.1920.0040.194
plotDensity0.0840.0000.086
plotGammaFit8.4130.0048.420
plotHousekeepingGene0.1800.0000.182
plotSampleRelation1.3280.0041.335
plotStringencyGene0.1840.0000.186
plotVST0.3960.0080.406
probeID2nuID7.6000.0167.628
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID6.8570.0166.881
vst0.7480.0080.757