Package: lumi

Version: 2.8.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.8.0.tar.gz

StartedAt: 2012-09-24 01:57:57 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 02:10:27 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 749.2 seconds

RetCode: 0

Status:  OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/lumi.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘2.8.0’
* 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 10.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    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 ... OK
* 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 installed files from ‘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

NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘image’ when loading ‘graphics’
Warning: replacing previous import ‘density’ when loading ‘stats’
Warning: replacing previous import ‘residuals’ when loading ‘stats’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘IlluminaAnnotation.Rnw’ 
   ‘lumi.Rnw’ 
   ‘lumi_VST_evaluation.Rnw’ 
   ‘methylationAnalysis.Rnw’ 
** testing if installed package can be loaded
Warning: replacing previous import ‘image’ when loading ‘graphics’
Warning: replacing previous import ‘density’ when loading ‘stats’
Warning: replacing previous import ‘residuals’ when loading ‘stats’

* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	2.052	0.016	2.070
MAplot-methods	7.084	0.024	7.107
MethyGenoSet-class	0.000	0.000	0.001
addAnnotationInfo	0.108	0.004	0.114
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	3.700	0.024	3.738
adjColorBias.ssn	1.517	0.004	1.520
bgAdjust	0.092	0.004	0.096
bgAdjustMethylation	0.996	0.000	1.008
boxplot-MethyLumiM-methods	6.696	0.076	6.987
boxplot-methods	0.208	0.000	0.218
boxplotColorBias	1.108	0.008	1.176
density-methods	0.100	0.004	0.104
detectOutlier	0.116	0.008	0.124
detectionCall	0.148	0.012	0.167
estimateBeta	0.252	0.012	0.278
estimateIntensity	0.324	0.020	0.358
estimateLumiCV	0.100	0.008	0.112
estimateM	2.312	0.076	2.390
estimateMethylationBG	0.256	0.012	0.269
example.lumi	0.084	0.000	0.082
example.lumiMethy	0.108	0.000	0.107
example.methyTitration	0.188	0.004	0.193
gammaFitEM	7.337	0.016	7.354
getChipInfo	5.676	0.132	6.034
getControlData	0.628	0.004	0.948
getControlProbe	0.148	0.000	0.150
getControlType	0.136	0.012	0.152
getNuIDMappingInfo	30.082	0.036	30.198
hist-methods	0.136	0.004	0.138
id2seq	0.004	0.000	0.001
inverseVST	0.700	0.008	0.710
is.nuID	0.000	0.000	0.001
lumiB	0.100	0.000	0.101
lumiExpresso	0.528	0.004	0.531
lumiMethyB	0.104	0.004	0.109
lumiMethyC	3.448	0.004	3.458
lumiMethyN	0.244	0.000	0.241
lumiMethyStatus	162.151	0.032	163.573
lumiN	0.756	0.004	0.827
lumiQ	0.336	0.004	0.351
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.496	0.012	0.554
methylationCall	10.148	0.020	10.225
normalizeMethylation.quantile	0.940	0.008	0.950
normalizeMethylation.ssn	0.416	0.008	0.429
nuID2EntrezID	24.322	0.016	24.504
nuID2IlluminaID	7.512	0.004	7.533
nuID2RefSeqID	25.866	0.000	26.077
nuID2probeID	5.480	0.008	5.585
nuID2targetID	5.273	0.004	5.280
pairs-methods	1.992	0.008	2.010
plot-methods	2.352	0.016	2.366
plotCDF	0.160	0.012	0.172
plotColorBias1D	0.396	0.004	0.404
plotColorBias2D	0.244	0.012	0.257
plotControlData	0.208	0.004	0.214
plotDensity	0.108	0.004	0.113
plotGammaFit	8.805	0.004	8.900
plotHousekeepingGene	0.220	0.000	0.229
plotSampleRelation	0.952	0.008	0.963
plotStringencyGene	0.220	0.000	0.222
plotVST	0.468	0.008	0.478
probeID2nuID	5.800	0.008	5.819
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.000	0.000	0.001
targetID2nuID	5.020	0.012	5.046
vst	0.676	0.008	0.692