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Package 259/467HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 2.4.0
Pan Du
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/lumi
Last Changed Rev: 56142 / Revision: 59457
Last Changed Date: 2011-06-13 11:59:45 -0700 (Mon, 13 Jun 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: lumi
Version: 2.4.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.4.0.tar.gz
StartedAt: 2011-10-20 15:44:33 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 15:56:27 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 714.3 seconds
RetCode: 0
Status:  OK 
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/lumi.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.4.0'
* checking package namespace 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 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 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 4761Kb to 728Kb
     compacted 'methylationAnalysis.pdf' from 8.0Mb to 2.0Mb
  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
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-class1.0650.0491.150
MAplot-methods8.7780.3599.752
addColorChannelInfo0.1480.0060.163
addControlData2lumi0.0000.0010.000
addNuID2lumi0.0010.0000.001
adjColorBias.quantile1.4070.2081.720
adjColorBias.ssn1.2170.1731.450
bgAdjust0.1430.0080.157
bgAdjustMethylation0.7070.0860.819
boxplot-MethyLumiM-methods2.7610.2343.267
boxplot-methods0.3610.0240.443
boxplotColorBias0.8990.1321.171
density-methods0.1590.0120.178
detectOutlier0.1790.0320.227
detectionCall0.2630.0120.308
estimateBeta0.3660.0440.441
estimateIntensity0.4880.0500.557
estimateLumiCV0.1630.0150.186
estimateM2.3090.2412.726
estimateMethylationBG0.3870.0500.438
example.lumi0.1380.0050.149
example.lumiMethy0.1490.0060.157
example.methyTitration0.2500.0100.261
gammaFitEM 8.556 6.67415.477
getChipInfo6.9350.7978.077
getControlData0.7920.0410.845
getControlProbe0.1810.0080.192
getControlType0.2330.0120.246
getNuIDMappingInfo23.317 0.13223.665
hist-methods0.2290.0110.241
id2seq0.0010.0000.001
inverseVST0.9920.0921.089
is.nuID0.0010.0000.001
lumiB0.1530.0110.166
lumiExpresso0.4790.0740.556
lumiMethyB0.1580.0070.166
lumiMethyC1.3360.2141.569
lumiMethyN0.1960.0120.214
lumiMethyStatus162.775112.126288.672
lumiN1.2110.1451.368
lumiQ0.5490.0620.620
lumiR0.0000.0000.001
lumiR.batch000
lumiT0.5640.0840.650
methylationCall11.771 6.90219.276
normalizeMethylation.quantile0.2840.0320.317
normalizeMethylation.ssn0.4960.0860.590
nuID2EntrezID17.210 0.08417.388
nuID2IlluminaID8.4600.3608.869
nuID2RefSeqID26.810 0.13527.303
nuID2probeID7.9030.3498.701
nuID2targetID7.5760.3388.376
pairs-methods2.0120.2642.392
plot-methods3.6670.2344.020
plotCDF0.2770.0330.404
plotColorBias1D0.4660.0690.581
plotColorBias2D0.2090.0130.224
plotControlData0.3620.0140.385
plotDensity0.1930.0170.216
plotGammaFit11.790 7.22520.565
plotHousekeepingGene0.3630.0140.430
plotSampleRelation2.1220.0312.154
plotStringencyGene0.3350.0080.343
plotVST0.7020.1010.807
probeID2nuID7.7470.3518.172
produceGEOPlatformFile0.0000.0000.001
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id0.0010.0000.001
targetID2nuID7.3730.3457.872
vst1.1260.0951.238