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Package 263/472HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 2.5.1
Pan Du
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi
Last Changed Rev: 56090 / Revision: 56351
Last Changed Date: 2011-06-09 17:02:42 -0700 (Thu, 09 Jun 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 
moscato1 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: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.5.1.tar.gz
StartedAt: 2011-06-22 03:51:33 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 04:03:42 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 728.8 seconds
RetCode: 0
Status:  OK 
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/lumi.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* 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 ‘2.5.1’
* 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 12.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    8.2Mb
* 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: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 sizes of PDF files under ‘inst/doc’ ... 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-class1.0930.0491.193
MAplot-methods8.9210.3509.540
addColorChannelInfo0.1520.0070.160
addControlData2lumi0.0000.0010.001
addNuID2lumi0.0000.0000.001
adjColorBias.quantile2.4030.5963.023
adjColorBias.ssn1.3250.1641.529
bgAdjust0.1370.0070.181
bgAdjustMethylation0.6390.0880.878
boxplot-MethyLumiM-methods2.8600.2233.215
boxplot-methods0.3520.0230.435
boxplotColorBias0.9100.1321.054
density-methods0.1590.0130.182
detectOutlier0.1740.0330.214
detectionCall0.2650.0110.277
estimateBeta0.3610.0410.423
estimateIntensity0.4910.0470.546
estimateLumiCV0.1880.0150.204
estimateM2.3640.2322.632
estimateMethylationBG0.3980.0540.458
example.lumi0.1380.0050.144
example.lumiMethy0.1500.0060.157
example.methyTitration0.2450.0080.266
gammaFitEM 8.595 6.57316.303
getChipInfo6.8150.7807.910
getControlData0.9010.0420.956
getControlProbe0.2600.0070.268
getControlType0.1870.0080.197
getNuIDMappingInfo24.157 0.17124.613
hist-methods0.1610.0120.173
id2seq0.0010.0000.001
inverseVST0.6400.0960.745
is.nuID0.0020.0010.001
lumiB0.1450.0080.154
lumiExpresso0.6710.0830.779
lumiMethyB0.1510.0070.173
lumiMethyC3.0360.6153.775
lumiMethyN0.1940.0100.203
lumiMethyStatus173.126108.785296.080
lumiN1.4340.1531.772
lumiQ0.3970.0710.556
lumiR0.0000.0000.001
lumiR.batch0.0000.0000.001
lumiT0.6150.0930.716
methylationCall11.430 6.59719.537
normalizeMethylation.quantile0.2780.0340.344
normalizeMethylation.ssn0.5060.0900.657
nuID2EntrezID17.499 0.11918.133
nuID2IlluminaID8.7770.3609.340
nuID2RefSeqID28.481 0.12728.921
nuID2probeID8.2540.3438.719
nuID2targetID7.7670.3488.185
pairs-methods1.9520.2692.261
plot-methods3.5850.2053.886
plotCDF0.2840.0300.317
plotColorBias1D0.4380.0600.503
plotColorBias2D0.6460.0120.661
plotControlData0.3460.0100.357
plotDensity0.1950.0130.208
plotGammaFit11.729 6.86519.028
plotHousekeepingGene0.3550.0120.368
plotSampleRelation2.1650.0322.219
plotStringencyGene0.3360.0080.347
plotVST0.6590.0960.762
probeID2nuID8.0820.3418.510
produceGEOPlatformFile000
produceGEOSubmissionFile0.0000.0000.001
produceMethylationGEOSubmissionFile0.0000.0010.000
seq2id0.0010.0000.001
targetID2nuID8.0730.3438.552
vst0.9270.1071.043