BioC 2.12: CHECK report for lumi on petty

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: 2013-10-08 22:57:30 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:15:24 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 1073.8 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 3.0.1 (2013-05-16)
* 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 ... [45s/46s] 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NB: .First.lib is obsolete and will not be used in R 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [8m/10m] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
lumiMethyStatus    180.601 27.345 240.753
getNuIDMappingInfo  41.641  0.221  41.977
nuID2RefSeqID       38.680  0.175  46.545
nuID2EntrezID       28.259  0.189  48.498
plotGammaFit        12.477  1.380  14.717
methylationCall     11.848  1.149  23.259
gammaFitEM          10.530  1.700  12.262
getChipInfo         11.233  0.612  12.181
MAplot-methods      11.067  0.160  11.313
nuID2IlluminaID     10.303  0.310  15.108
nuID2probeID         8.560  0.265   8.981
nuID2targetID        8.538  0.282  16.212
probeID2nuID         7.833  0.282   9.461
targetID2nuID        7.343  0.272  12.557
LumiBatch-class      4.915  0.106   5.030
plot-methods         4.668  0.099   5.550
* 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	4.915	0.106	5.030
MAplot-methods	11.067	0.160	11.313
addAnnotationInfo	0.117	0.014	0.131
addControlData2lumi	0.010	0.003	0.013
addNuID2lumi	0.020	0.005	0.025
adjColorBias.quantile	4.109	0.154	4.311
adjColorBias.ssn	1.837	0.067	1.928
bgAdjust	0.154	0.021	0.180
bgAdjustMethylation	1.088	0.027	1.127
boxplot-MethyLumiM-methods	1.940	0.053	2.012
boxplot-methods	0.368	0.023	0.392
boxplotColorBias	1.951	0.049	2.021
density-methods	0.175	0.026	0.204
detectOutlier	0.185	0.029	0.226
detectionCall	0.299	0.033	0.332
estimateBeta	0.218	0.029	0.246
estimateIntensity	1.085	0.027	1.118
estimateLumiCV	0.206	0.022	0.229
estimateM	1.872	0.063	1.973
estimateMethylationBG	1.000	0.024	1.025
example.lumi	0.151	0.028	0.179
example.lumiMethy	0.110	0.012	0.122
example.methyTitration	0.339	0.030	0.370
gammaFitEM	10.530	1.700	12.262
getChipInfo	11.233	0.612	12.181
getControlData	1.728	0.094	1.826
getControlProbe	0.380	0.017	0.397
getControlType	0.459	0.014	0.475
getNuIDMappingInfo	41.641	0.221	41.977
hist-methods	0.246	0.023	0.270
id2seq	0.050	0.006	0.057
inverseVST	2.194	0.077	2.275
is.nuID	0.005	0.007	0.011
lumiB	0.148	0.019	0.167
lumiExpresso	0.484	0.037	0.525
lumiMethyB	0.129	0.013	0.143
lumiMethyC	3.320	0.163	3.493
lumiMethyN	0.162	0.018	0.179
lumiMethyStatus	180.601	27.345	240.753
lumiN	2.014	0.078	4.154
lumiQ	0.480	0.068	2.874
lumiR	0.004	0.005	0.011
lumiR.batch	0.002	0.004	0.010
lumiT	0.785	0.077	3.391
methylationCall	11.848	1.149	23.259
normalizeMethylation.quantile	0.418	0.052	1.651
normalizeMethylation.ssn	0.518	0.041	1.113
nuID2EntrezID	28.259	0.189	48.498
nuID2IlluminaID	10.303	0.310	15.108
nuID2RefSeqID	38.680	0.175	46.545
nuID2probeID	8.560	0.265	8.981
nuID2targetID	8.538	0.282	16.212
pairs-methods	1.706	0.124	3.215
plot-methods	4.668	0.099	5.550
plotCDF	0.311	0.024	0.338
plotColorBias1D	0.699	0.025	0.736
plotColorBias2D	0.418	0.020	0.442
plotControlData	0.430	0.016	0.461
plotDensity	0.264	0.026	0.291
plotGammaFit	12.477	1.380	14.717
plotHousekeepingGene	0.393	0.017	0.451
plotSampleRelation	2.440	0.028	2.680
plotStringencyGene	0.383	0.015	0.423
plotVST	0.702	0.039	0.934
probeID2nuID	7.833	0.282	9.461
produceGEOPlatformFile	0.002	0.004	0.016
produceGEOSubmissionFile	0.003	0.004	0.007
produceMethylationGEOSubmissionFile	0.003	0.004	0.022
seq2id	0.004	0.004	0.018
targetID2nuID	7.343	0.272	12.557
vst	1.425	0.040	2.429