BioC 2.11: CHECK report for lumi on perceval

Package: lumi

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.10.0.tar.gz

StartedAt: 2013-03-25 00:15:23 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:28:05 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 762.2 seconds

RetCode: 0

Status: OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/lumi.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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   2.3Mb
    doc    7.8Mb
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user  system elapsed
lumiMethyStatus    150.133 127.346 295.017
nuID2RefSeqID       22.891   0.118  23.068
nuID2EntrezID       16.935   0.110  17.194
methylationCall      9.411   7.545  18.096
getNuIDMappingInfo  16.547   0.180  17.347
plotGammaFit         9.338   6.895  16.789
gammaFitEM           7.668   6.676  15.013
getChipInfo          7.980   0.871  10.094
nuID2IlluminaID      7.587   0.369   8.089
MAplot-methods       7.138   0.387   7.791
nuID2targetID        7.133   0.322   7.542
nuID2probeID         6.869   0.326   7.274
probeID2nuID         6.457   0.320   6.826
targetID2nuID        6.460   0.313   6.803
* 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
  '/Users/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	2.982	0.130	3.205
MAplot-methods	7.138	0.387	7.791
addAnnotationInfo	0.145	0.013	0.174
addControlData2lumi	0	0	0
addNuID2lumi	0.000	0.001	0.000
adjColorBias.quantile	3.018	0.733	3.940
adjColorBias.ssn	1.192	0.172	1.428
bgAdjust	0.118	0.013	0.136
bgAdjustMethylation	0.730	0.104	0.913
boxplot-MethyLumiM-methods	1.563	0.123	1.733
boxplot-methods	0.618	0.037	0.679
boxplotColorBias	0.605	0.151	0.804
density-methods	0.465	0.024	0.492
detectOutlier	0.132	0.027	0.164
detectionCall	0.216	0.026	0.252
estimateBeta	0.210	0.043	0.257
estimateIntensity	0.763	0.070	0.841
estimateLumiCV	0.147	0.018	0.170
estimateM	1.504	0.117	1.640
estimateMethylationBG	0.315	0.063	0.387
example.lumi	0.110	0.010	0.121
example.lumiMethy	0.142	0.011	0.156
example.methyTitration	0.248	0.019	0.271
gammaFitEM	7.668	6.676	15.013
getChipInfo	7.980	0.871	10.094
getControlData	1.740	0.072	1.927
getControlProbe	0.154	0.012	0.232
getControlType	0.150	0.012	0.166
getNuIDMappingInfo	16.547	0.180	17.347
hist-methods	0.166	0.019	0.187
id2seq	0.001	0.001	0.001
inverseVST	1.073	0.122	1.220
is.nuID	0.001	0.000	0.001
lumiB	0.169	0.018	0.191
lumiExpresso	0.640	0.096	0.746
lumiMethyB	0.149	0.014	0.167
lumiMethyC	2.720	0.777	3.606
lumiMethyN	0.176	0.018	0.201
lumiMethyStatus	150.133	127.346	295.017
lumiN	1.211	0.165	1.417
lumiQ	0.377	0.085	0.493
lumiR	0.001	0.000	0.000
lumiR.batch	0	0	0
lumiT	0.609	0.123	0.763
methylationCall	9.411	7.545	18.096
normalizeMethylation.quantile	1.367	0.143	1.524
normalizeMethylation.ssn	0.377	0.080	0.472
nuID2EntrezID	16.935	0.110	17.194
nuID2IlluminaID	7.587	0.369	8.089
nuID2RefSeqID	22.891	0.118	23.068
nuID2probeID	6.869	0.326	7.274
nuID2targetID	7.133	0.322	7.542
pairs-methods	1.981	0.272	2.294
plot-methods	3.424	0.221	3.684
plotCDF	0.291	0.032	0.349
plotColorBias1D	0.938	0.068	1.016
plotColorBias2D	0.279	0.021	0.305
plotControlData	0.256	0.013	0.271
plotDensity	0.169	0.020	0.191
plotGammaFit	9.338	6.895	16.789
plotHousekeepingGene	0.260	0.011	0.272
plotSampleRelation	1.119	0.031	1.166
plotStringencyGene	0.225	0.009	0.236
plotVST	0.549	0.103	0.678
probeID2nuID	6.457	0.320	6.826
produceGEOPlatformFile	0.000	0.000	0.001
produceGEOSubmissionFile	0.001	0.000	0.000
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.001	0.000	0.001
targetID2nuID	6.460	0.313	6.803
vst	1.355	0.107	1.472

Summary

Command output