BioC 2.11: CHECK report for lumi on lamb1

Package: lumi

Version: 2.10.0

Command: /home/biocbuild/bbs-2.11-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.10.0.tar.gz

StartedAt: 2013-03-25 02:40:33 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:51:01 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 628.0 seconds

RetCode: 0

Status: OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.11-bioc/meat/lumi.Rcheck’
* using R version 2.15.3 (2013-03-01)
* 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 ‘2.10.0’
* 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 for left-over 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 ... NOTE
getChrInfo: no visible global function definition for ‘space’
getChrInfo: no visible global function definition for ‘GRanges’
getChrInfo: no visible global function definition for ‘IRanges’
* checking Rd files ... NOTE
prepare_Rd: getChrInfo.Rd:26-28: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:32-34: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:41-43: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:44-47: Dropping empty section \examples
prepare_Rd: importMethyIDAT.Rd:47-50: 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
lumiMethyStatus    164.279  0.148 167.614
nuID2RefSeqID       30.318  0.052  30.801
getNuIDMappingInfo  21.369  0.020  22.021
nuID2EntrezID       20.618  0.012  20.793
plotGammaFit        12.161  0.016  12.217
methylationCall      9.600  0.024   9.669
getChipInfo          9.021  0.204   9.797
gammaFitEM           8.737  0.008   8.981
targetID2nuID        7.512  0.016   7.604
nuID2IlluminaID      7.328  0.024   7.457
nuID2targetID        7.065  0.012   7.094
probeID2nuID         7.001  0.020   7.088
nuID2probeID         6.960  0.016   7.023
MAplot-methods       5.565  0.028   5.686
* 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 were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.11-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’
** 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’

* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	3.332	0.060	3.461
MAplot-methods	5.565	0.028	5.686
addAnnotationInfo	0.096	0.008	0.119
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	3.724	0.020	3.747
adjColorBias.ssn	1.124	0.004	1.144
bgAdjust	0.080	0.004	0.094
bgAdjustMethylation	0.328	0.000	0.340
boxplot-MethyLumiM-methods	1.604	0.000	1.626
boxplot-methods	0.248	0.000	0.247
boxplotColorBias	1.368	0.004	1.373
density-methods	0.108	0.000	0.211
detectOutlier	0.120	0.000	0.201
detectionCall	0.168	0.000	0.350
estimateBeta	0.696	0.000	0.726
estimateIntensity	0.788	0.000	0.804
estimateLumiCV	0.104	0.004	0.108
estimateM	1.152	0.020	1.264
estimateMethylationBG	0.808	0.004	0.889
example.lumi	0.084	0.000	0.117
example.lumiMethy	0.112	0.004	0.170
example.methyTitration	0.176	0.004	0.183
gammaFitEM	8.737	0.008	8.981
getChipInfo	9.021	0.204	9.797
getControlData	1.044	0.028	1.086
getControlProbe	0.204	0.000	0.205
getControlType	0.124	0.000	0.124
getNuIDMappingInfo	21.369	0.020	22.021
hist-methods	0.128	0.004	0.143
id2seq	0.000	0.000	0.001
inverseVST	1.080	0.000	1.091
is.nuID	0.000	0.000	0.001
lumiB	0.084	0.008	0.094
lumiExpresso	0.464	0.008	0.485
lumiMethyB	0.104	0.000	0.108
lumiMethyC	2.960	0.016	2.992
lumiMethyN	0.132	0.004	0.136
lumiMethyStatus	164.279	0.148	167.614
lumiN	0.852	0.008	0.911
lumiQ	0.372	0.004	0.378
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.472	0.012	0.541
methylationCall	9.600	0.024	9.669
normalizeMethylation.quantile	0.804	0.056	1.154
normalizeMethylation.ssn	0.316	0.012	0.396
nuID2EntrezID	20.618	0.012	20.793
nuID2IlluminaID	7.328	0.024	7.457
nuID2RefSeqID	30.318	0.052	30.801
nuID2probeID	6.960	0.016	7.023
nuID2targetID	7.065	0.012	7.094
pairs-methods	1.264	0.008	1.309
plot-methods	2.700	0.028	2.732
plotCDF	0.228	0.000	0.284
plotColorBias1D	0.424	0.008	0.438
plotColorBias2D	0.260	0.004	0.266
plotControlData	0.256	0.020	0.292
plotDensity	0.120	0.004	0.135
plotGammaFit	12.161	0.016	12.217
plotHousekeepingGene	0.184	0.004	0.205
plotSampleRelation	1.032	0.008	1.056
plotStringencyGene	0.184	0.000	0.196
plotVST	0.524	0.004	0.527
probeID2nuID	7.001	0.020	7.088
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	7.512	0.016	7.604
vst	0.808	0.008	0.818

Summary

Command output