Package: lumi

Version: 1.14.0

Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings lumi_1.14.0.tar.gz

StartedAt: 2010-10-04 17:31:15 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 17:34:48 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 213.7 seconds

RetCode: 0

Status:  OK

CheckDir: lumi.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory 'D:/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

* 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)

name	user	system	elapsed
LumiBatch-class	1.20	0.02	1.22
MAplot-methods	7.17	0.00	7.17
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
bgAdjust	0.07	0.01	0.08
boxplot-methods	0.26	0.02	0.28
density-methods	0.24	0.00	0.23
detectOutlier	0.09	0.00	0.10
detectionCall	0.16	0.02	0.17
estimateLumiCV	0.09	0.00	0.09
example.lumi	0.08	0.00	0.08
getChipInfo	9.33	0.29	11.66
getControlData	1.17	0.00	1.17
getControlProbe	0.19	0.00	0.19
getControlType	0.2	0.0	0.2
getNuIDMappingInfo	5.55	0.02	5.58
hist-methods	0.13	0.00	0.13
id2seq	0	0	0
inverseVST	0.61	0.00	0.65
is.nuID	0	0	0
lumiB	0.09	0.00	0.10
lumiExpresso	0.7	0.0	0.7
lumiN	1.02	0.01	1.13
lumiQ	0.30	0.00	0.29
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.48	0.00	0.49
nuID2EntrezID	5.11	0.05	5.15
nuID2IlluminaID	7.50	0.00	7.58
nuID2RefSeqID	5.66	0.00	5.66
nuID2probeID	6.90	0.02	6.92
nuID2targetID	6.70	0.00	6.71
pairs-methods	1.45	0.00	1.45
plot-methods	2.74	0.01	2.75
plotCDF-methods	0.17	0.00	0.17
plotControlData	0.23	0.00	0.23
plotHousekeepingGene	0.22	0.00	0.22
plotSampleRelation	1.62	0.00	1.63
plotStringencyGene	0.21	0.02	0.22
plotVST	0.51	0.01	0.53
probeID2nuID	6.94	0.00	6.93
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	7.34	0.00	7.35
vst	0.72	0.00	0.72