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Package 232/419HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 2.2.1
Pan Du
Snapshot Date: 2011-04-06 23:24:01 -0700 (Wed, 06 Apr 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/lumi
Last Changed Rev: 51657 / Revision: 54588
Last Changed Date: 2010-12-21 12:47:03 -0800 (Tue, 21 Dec 2010)
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 

Summary

Package: lumi
Version: 2.2.1
Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.2.1.tar.gz
StartedAt: 2011-04-07 07:23:17 -0700 (Thu, 07 Apr 2011)
EndedAt: 2011-04-07 07:27:41 -0700 (Thu, 07 Apr 2011)
EllapsedTime: 263.9 seconds
RetCode: 0
Status:  OK 
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/lumi.Rcheck’
* using R version 2.12.2 (2011-02-25)
* 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 ‘2.2.1’
* 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 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: 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:25-26: 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: 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:30-32: 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: 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:26: 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
  'openVignette()'. 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-class1.1480.0121.161
MAplot-methods6.8120.0206.836
MethyLumiM-class0.0000.0000.002
addColorChannelInfo0.0640.0000.062
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile0.8400.0040.844
adjColorBias.ssn1.0480.0081.057
bgAdjust0.0600.0000.063
bgAdjustMethylation0.4560.0040.460
boxplot-MethyLumiM-methods3.0010.0563.069
boxplot-methods0.2120.0000.215
boxplotColorBias0.6280.0040.635
density-methods0.0760.0000.077
detectOutlier0.0800.0080.086
detectionCall0.1120.0000.113
estimateBeta0.2040.0000.202
estimateIntensity0.2840.0040.287
estimateLumiCV0.0840.0000.084
estimateM2.1920.0642.256
estimateMethylationBG0.2280.0000.229
example.lumi0.0640.0000.061
example.lumiMethy0.0600.0000.061
example.methyTitration0.1120.0000.111
getChipInfo5.7920.1606.269
getControlData0.7680.0080.777
getControlProbe0.2000.0000.198
getControlType0.1920.0000.191
getNuIDMappingInfo22.418 0.01222.439
hist-methods0.1120.0120.126
id2seq0.0000.0000.001
inverseVST0.6840.0040.696
is.nuID0.0000.0000.001
lumiB0.0640.0000.064
lumiExpresso0.3240.0000.347
lumiMethyB0.060.000.06
lumiMethyC0.8040.0040.810
lumiMethyN0.0680.0080.088
lumiN0.8120.0040.827
lumiQ0.2560.0000.255
lumiR000
lumiR.batch000
lumiT0.5680.0120.580
normalizeMethylation.quantile0.1480.0000.152
normalizeMethylation.ssn0.2960.0000.298
nuID2EntrezID15.933 0.00415.932
nuID2IlluminaID7.9480.0087.955
nuID2RefSeqID22.530 0.00422.532
nuID2probeID7.2840.0087.291
nuID2targetID6.5690.0086.578
pairs-methods1.2040.0121.216
plot-methods2.5680.0042.571
plotCDF0.1280.0080.135
plotColorBias1D0.2320.0000.234
plotColorBias2D0.1040.0000.103
plotControlData0.1920.0000.193
plotDensity0.0840.0000.082
plotHousekeepingGene0.1960.0040.201
plotSampleRelation1.3280.0001.327
plotStringencyGene0.2000.0000.197
plotVST0.4120.0040.414
probeID2nuID6.2610.0086.268
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID6.5960.0006.594
vst0.8920.0000.894