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Package 287/514HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 2.6.0
Pan Du
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/lumi
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: lumi
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.6.0.tar.gz
StartedAt: 2012-03-24 02:11:43 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 02:26:07 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 864.4 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 2.14.2 (2012-02-29)
* 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 '2.6.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'lumi' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    7.7Mb
* 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: addAnnotationInfo.Rd:17-20: 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                             old_size new_size compress
  example.lumi.rda              940Kb    405Kb       xz
  example.lumiMethy.rda         1.1Mb    903Kb       xz
  example.methyTitration.rda    1.5Mb    1.1Mb       xz
* 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
** 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-class1.3400.0521.407
MAplot-methods9.2130.3619.644
addAnnotationInfo0.1570.0070.166
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile2.2530.2762.566
adjColorBias.ssn1.5770.1751.772
bgAdjust0.1430.0080.151
bgAdjustMethylation0.9250.0851.011
boxplot-MethyLumiM-methods3.7780.2414.184
boxplot-methods0.3290.0230.360
boxplotColorBias0.9520.1341.099
density-methods0.1630.0140.184
detectOutlier0.1840.0340.219
detectionCall0.2700.0140.285
estimateBeta0.3570.0440.406
estimateIntensity0.5040.0550.562
estimateLumiCV0.4080.0250.444
estimateM2.7420.2303.011
estimateMethylationBG0.3750.0520.427
example.lumi0.1380.0060.148
example.lumiMethy0.1530.0070.161
example.methyTitration0.2540.0110.266
gammaFitEM 8.659 6.58515.370
getChipInfo6.8210.8068.130
getControlData0.6820.0610.748
getControlProbe0.2290.0080.240
getControlType0.1700.0060.197
getNuIDMappingInfo34.163 0.17135.325
hist-methods0.2940.0160.312
id2seq0.0010.0010.002
inverseVST0.8530.0961.009
is.nuID0.0010.0000.001
lumiB0.1470.0070.155
lumiExpresso0.7450.0790.846
lumiMethyB0.1520.0060.158
lumiMethyC2.8530.2543.149
lumiMethyN0.1970.0120.209
lumiMethyStatus188.435132.358335.867
lumiN1.1540.1701.387
lumiQ0.5340.0840.625
lumiR0.0000.0010.001
lumiR.batch000
lumiT0.8290.1260.970
methylationCall11.353 7.62619.555
normalizeMethylation.quantile0.2830.0400.327
normalizeMethylation.ssn0.7900.1020.910
nuID2EntrezID23.220 0.11123.470
nuID2IlluminaID7.2740.3527.712
nuID2RefSeqID25.372 0.12425.756
nuID2probeID7.4210.3397.803
nuID2targetID6.7990.3527.230
pairs-methods2.5620.2812.889
plot-methods4.8650.2715.196
plotCDF0.7560.0390.910
plotColorBias1D0.5360.0720.611
plotColorBias2D0.3460.0210.367
plotControlData0.3590.0180.377
plotDensity0.1970.0140.212
plotGammaFit11.767 7.51219.785
plotHousekeepingGene0.3660.0130.388
plotSampleRelation1.5150.0351.620
plotStringencyGene0.3100.0080.319
plotVST0.7720.1130.899
probeID2nuID7.4570.3567.988
produceGEOPlatformFile000
produceGEOSubmissionFile0.0010.0000.000
produceMethylationGEOSubmissionFile0.0000.0010.000
seq2id0.0010.0000.001
targetID2nuID7.3360.3407.741
vst0.8710.1181.005