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Package 217/389HostnameOS / ArchBUILDCHECKBUILD BIN
lumi 1.14.0
Pan Du
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/lumi
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / 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: 1.14.0
Command: E:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings lumi_1.14.0.tar.gz
StartedAt: 2010-10-04 18:56:18 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 18:59:31 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 192.8 seconds
RetCode: 0
Status:  OK  
CheckDir: lumi.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.6-bioc/meat/lumi.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '1.14.0'
* 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 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: addControlData2lumi.Rd:22: Dropping empty section \references
prepare_Rd: affyExpresso.Rd:36: Dropping empty section \references
prepare_Rd: affyExpresso.Rd:42-45: Dropping empty section \examples
prepare_Rd: affyVstRma.Rd:26: Dropping empty section \references
prepare_Rd: affyVstRma.Rd:32-35: Dropping empty section \examples
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: lumiN.Rd:28-30: Dropping empty section \note
prepare_Rd: lumiN.Rd:26: 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: 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: 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 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:

* install options are ' --no-html'

* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: AnnotationDbi
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

This is mgcv 1.6-2. For overview type 'help("mgcv-package")'.
Loading required package: DBI
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-class0.980.031.01
MAplot-methods6.600.016.65
addControlData2lumi000
addNuID2lumi000
bgAdjust0.070.000.08
boxplot-methods0.250.000.25
density-methods0.100.000.09
detectOutlier0.220.000.22
detectionCall0.150.000.15
estimateLumiCV0.100.020.11
example.lumi0.070.000.08
getChipInfo7.500.188.03
getControlData1.050.021.06
getControlProbe0.200.000.21
getControlType0.190.010.20
getNuIDMappingInfo3.410.033.47
hist-methods0.120.000.12
id2seq000
inverseVST0.640.020.69
is.nuID000
lumiB0.250.010.27
lumiExpresso0.350.020.37
lumiN1.140.001.14
lumiQ0.360.010.38
lumiR000
lumiR.batch000
lumiT0.580.020.59
nuID2EntrezID3.290.013.31
nuID2IlluminaID5.330.045.36
nuID2RefSeqID3.660.043.71
nuID2probeID4.550.024.59
nuID2targetID4.670.004.69
pairs-methods2.020.012.03
plot-methods2.530.052.60
plotCDF-methods0.260.000.26
plotControlData0.190.020.22
plotHousekeepingGene0.220.010.24
plotSampleRelation1.470.021.48
plotStringencyGene0.230.000.38
plotVST0.600.010.61
probeID2nuID4.870.004.87
produceGEOPlatformFile000
produceGEOSubmissionFile000
seq2id000
targetID2nuID5.580.016.03
vst0.590.020.61