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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: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.5.1.tar.gz
StartedAt: 2011-05-09 15:26:40 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 15:38:41 -0700 (Mon, 09 May 2011)
EllapsedTime: 721.0 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) (2011-04-24 r55634)
* 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 32.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc   28.6Mb
* 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’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘lumi.pdf’ from 12.8Mb to 2.4Mb
     compacted ‘lumi_VST_evaluation.pdf’ from 4715Kb to 649Kb
     compacted ‘methylationAnalysis.pdf’ from 7.9Mb to 1.8Mb
  consider running tools::compactPDF() on these files
* 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-class1.0770.0451.133
MAplot-methods8.7330.3419.160
addColorChannelInfo0.1540.0080.165
addControlData2lumi0.0000.0000.001
addNuID2lumi0.0010.0010.000
adjColorBias.quantile2.7740.5873.451
adjColorBias.ssn1.2230.1671.466
bgAdjust0.1380.0060.144
bgAdjustMethylation0.7320.0890.850
boxplot-MethyLumiM-methods2.8100.2383.272
boxplot-methods0.3520.0220.377
boxplotColorBias0.8900.1261.028
density-methods0.1590.0110.171
detectOutlier0.1740.0310.208
detectionCall0.2630.0110.275
estimateBeta0.3570.0400.398
estimateIntensity0.4860.0480.542
estimateLumiCV0.1880.0150.204
estimateM2.3390.2372.593
estimateMethylationBG0.3930.0520.448
example.lumi0.1440.0070.161
example.lumiMethy0.1540.0080.162
example.methyTitration0.2460.0090.260
gammaFitEM 8.567 6.65217.025
getChipInfo6.9400.7917.963
getControlData0.9720.0381.016
getControlProbe0.2610.0070.270
getControlType0.3110.0120.334
getNuIDMappingInfo22.848 0.16923.248
hist-methods0.1600.0120.172
id2seq0.0010.0000.002
inverseVST0.6880.1010.792
is.nuID0.0010.0000.001
lumiB0.1440.0070.150
lumiExpresso0.7240.0830.810
lumiMethyB0.1480.0050.153
lumiMethyC3.2800.5853.887
lumiMethyN0.1920.0100.203
lumiMethyStatus163.944111.466289.152
lumiN1.1810.1351.326
lumiQ0.3930.0630.470
lumiR0.0000.0000.001
lumiR.batch0.0000.0000.001
lumiT0.5830.0900.682
methylationCall10.730 6.54518.806
normalizeMethylation.quantile0.2730.0310.305
normalizeMethylation.ssn0.5190.0890.641
nuID2EntrezID16.451 0.10317.034
nuID2IlluminaID7.9680.3418.612
nuID2RefSeqID22.555 0.10623.022
nuID2probeID7.4900.3437.993
nuID2targetID7.8940.3398.332
pairs-methods2.3180.2772.639
plot-methods3.5930.2103.845
plotCDF0.2770.0330.311
plotColorBias1D0.4630.0660.535
plotColorBias2D0.6660.0180.686
plotControlData0.4000.0180.420
plotDensity0.1990.0140.216
plotGammaFit11.335 7.10618.830
plotHousekeepingGene0.3670.0110.380
plotSampleRelation2.3920.0382.446
plotStringencyGene0.3680.0090.377
plotVST0.6420.0880.738
probeID2nuID8.4390.3478.847
produceGEOPlatformFile0.0010.0000.001
produceGEOSubmissionFile0.0000.0000.001
produceMethylationGEOSubmissionFile0.0000.0000.001
seq2id0.0010.0000.001
targetID2nuID8.8360.3449.246
vst1.2810.1211.418