BioC 2.12: CHECK report for lumi on pelham

Package: lumi

Version: 2.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.12.0.tar.gz

StartedAt: 2013-05-01 07:33:27 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 07:48:04 -0700 (Wed, 01 May 2013)

EllapsedTime: 877.4 seconds

RetCode: 0

Status: OK

CheckDir: lumi.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.12.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'lumi' can be installed ... [39s/42s] OK
* checking installed package size ... NOTE
  installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    7.7Mb
* checking package directory ... 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
* checking Rd files ... NOTE
prepare_Rd: getChrInfo.Rd:23-25: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:29-31: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:38-40: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:41-44: Dropping empty section \examples
prepare_Rd: importMethyIDAT.Rd:44-47: 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 ... [442s/459s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
lumiMethyStatus       181.936 11.627 199.353
getNuIDMappingInfo     30.155  0.279  31.097
nuID2EntrezID          23.269  0.251  23.922
nuID2RefSeqID          22.056  0.221  22.588
getChipInfo            11.662  0.669  13.720
plotGammaFit           11.448  0.826  12.536
methylationCall        11.056  0.908  12.168
gammaFitEM             10.090  0.544  10.841
nuID2probeID            9.700  0.347  10.166
nuID2targetID           9.612  0.331  10.333
MAplot-methods          9.381  0.177  11.639
nuID2IlluminaID         9.106  0.336   9.627
probeID2nuID            8.526  0.330   9.147
targetID2nuID           8.021  0.341   8.552
plot-methods            5.076  0.106   5.308
adjColorBias.quantile   4.510  0.110   5.274
* 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-2.12-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 'nleqslv' when loading 'nleqslv'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'image' when loading 'graphics'
Warning: replacing previous import 'nleqslv' when loading 'nleqslv'
Warning: ignoring .First.lib() for package 'lumi'
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	3.782	0.110	4.505
MAplot-methods	9.381	0.177	11.639
addAnnotationInfo	0.645	0.016	0.721
addControlData2lumi	0.010	0.004	0.014
addNuID2lumi	0.009	0.006	0.021
adjColorBias.quantile	4.510	0.110	5.274
adjColorBias.ssn	1.712	0.056	1.949
bgAdjust	0.135	0.019	0.211
bgAdjustMethylation	0.439	0.030	0.554
boxplot-MethyLumiM-methods	1.662	0.064	2.017
boxplot-methods	0.337	0.025	0.424
boxplotColorBias	1.321	0.058	1.546
density-methods	0.721	0.033	0.911
detectOutlier	0.172	0.035	0.389
detectionCall	0.260	0.033	0.293
estimateBeta	0.188	0.024	0.214
estimateIntensity	0.422	0.031	0.457
estimateLumiCV	0.168	0.021	0.190
estimateM	1.613	0.066	1.700
estimateMethylationBG	0.360	0.024	0.384
example.lumi	0.138	0.020	0.158
example.lumiMethy	0.109	0.011	0.119
example.methyTitration	0.270	0.031	0.308
gammaFitEM	10.090	0.544	10.841
getChipInfo	11.662	0.669	13.720
getControlData	1.562	0.095	1.768
getControlProbe	0.353	0.018	0.391
getControlType	0.418	0.018	0.485
getNuIDMappingInfo	30.155	0.279	31.097
hist-methods	0.247	0.025	0.276
id2seq	0.058	0.007	0.067
inverseVST	1.945	0.067	2.082
is.nuID	0.020	0.013	0.032
lumiB	0.124	0.017	0.142
lumiExpresso	0.443	0.047	0.497
lumiMethyB	0.105	0.012	0.120
lumiMethyC	2.499	0.082	2.622
lumiMethyN	0.775	0.024	0.805
lumiMethyStatus	181.936	11.627	199.353
lumiN	1.039	0.045	1.102
lumiQ	0.497	0.036	0.549
lumiR	0.003	0.004	0.008
lumiR.batch	0.003	0.005	0.009
lumiT	0.724	0.041	0.807
methylationCall	11.056	0.908	12.168
normalizeMethylation.quantile	0.389	0.043	0.437
normalizeMethylation.ssn	1.069	0.042	1.131
nuID2EntrezID	23.269	0.251	23.922
nuID2IlluminaID	9.106	0.336	9.627
nuID2RefSeqID	22.056	0.221	22.588
nuID2probeID	9.700	0.347	10.166
nuID2targetID	9.612	0.331	10.333
pairs-methods	1.816	0.099	1.940
plot-methods	5.076	0.106	5.308
plotCDF	0.222	0.026	0.258
plotColorBias1D	0.444	0.024	0.480
plotColorBias2D	0.248	0.018	0.273
plotControlData	0.359	0.022	0.550
plotDensity	0.198	0.022	0.224
plotGammaFit	11.448	0.826	12.536
plotHousekeepingGene	0.356	0.019	0.384
plotSampleRelation	1.308	0.025	1.360
plotStringencyGene	0.338	0.015	0.364
plotVST	0.732	0.041	0.810
probeID2nuID	8.526	0.330	9.147
produceGEOPlatformFile	0.003	0.004	0.006
produceGEOSubmissionFile	0.003	0.006	0.008
produceMethylationGEOSubmissionFile	0.004	0.009	0.013
seq2id	0.017	0.010	0.027
targetID2nuID	8.021	0.341	8.552
vst	1.600	0.036	1.687

Summary

Command output