BioC 2.12: CHECK report for lumi on petty

Package: lumi

Version: 2.11.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.11.6.tar.gz

StartedAt: 2013-03-25 03:22:27 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:37:19 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 891.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '2.11.6'
* 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 ... [48s/49s] OK
* checking installed package size ... NOTE
  installed size is 12.0Mb
  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NB: .First.lib is obsolete and will not be used in R 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 ... WARNING
Codoc mismatches from documentation object 'pairs-methods':
\S4method{pairs}{ExpressionSet}
  Code: function(x, ..., smoothScatter = FALSE, logMode = TRUE, subset
                 = 5000, fold = 2, dotColor = 1, highlight = NULL,
                 highlightColor = 2, main = NULL, checkTransform =
                 TRUE)
  Docs: function(x, ..., smoothScatter = FALSE, logMode = TRUE, subset
                 = 5000, fold = 2, dotColor = 1, highlight = NULL,
                 highlightColor = 2, main = NULL)
  Argument names in code not in docs:
    checkTransform

* 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 ... [501s/507s] OK
Examples with CPU or elapsed time > 5s
                      user  system elapsed
lumiMethyStatus    172.132 113.945 289.336
nuID2RefSeqID       24.249   0.072  24.321
plotGammaFit        11.561   7.699  19.400
methylationCall     10.605   6.504  17.310
getNuIDMappingInfo  16.072   0.184  16.256
gammaFitEM           8.570   6.554  15.361
nuID2EntrezID       12.402   0.079  12.488
getChipInfo          7.443   0.765   8.402
targetID2nuID        6.972   0.308   7.288
MAplot-methods       6.408   0.291   6.720
nuID2targetID        6.195   0.281   6.500
probeID2nuID         6.027   0.269   6.313
nuID2IlluminaID      5.635   0.256   5.909
nuID2probeID         5.263   0.228   5.504
* 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

WARNING: There was 1 warning.
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
   '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 'nleqslv' when loading 'nleqslv'
Warning: ignoring .First.lib() for package 'lumi'
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	3.034	0.107	3.145
MAplot-methods	6.408	0.291	6.720
addAnnotationInfo	0.106	0.017	0.123
addControlData2lumi	0.005	0.005	0.011
addNuID2lumi	0.007	0.007	0.015
adjColorBias.quantile	3.198	0.635	3.905
adjColorBias.ssn	1.170	0.146	1.322
bgAdjust	0.151	0.017	0.167
bgAdjustMethylation	0.685	0.070	0.755
boxplot-MethyLumiM-methods	1.306	0.087	1.397
boxplot-methods	0.605	0.029	0.636
boxplotColorBias	0.929	0.116	1.052
density-methods	0.152	0.020	0.172
detectOutlier	0.158	0.028	0.187
detectionCall	0.246	0.026	0.273
estimateBeta	0.518	0.041	0.562
estimateIntensity	0.708	0.051	0.761
estimateLumiCV	0.172	0.023	0.197
estimateM	1.631	0.094	1.730
estimateMethylationBG	0.297	0.054	0.353
example.lumi	0.131	0.015	0.147
example.lumiMethy	0.106	0.015	0.122
example.methyTitration	0.311	0.023	0.336
gammaFitEM	8.570	6.554	15.361
getChipInfo	7.443	0.765	8.402
getControlData	1.876	0.065	1.941
getControlProbe	0.213	0.022	0.235
getControlType	0.207	0.020	0.227
getNuIDMappingInfo	16.072	0.184	16.256
hist-methods	0.300	0.025	0.325
id2seq	0.586	0.014	0.601
inverseVST	1.168	0.123	1.292
is.nuID	0.006	0.009	0.015
lumiB	0.195	0.021	0.215
lumiExpresso	0.586	0.099	0.691
lumiMethyB	0.155	0.019	0.175
lumiMethyC	3.635	0.742	4.393
lumiMethyN	0.189	0.023	0.212
lumiMethyStatus	172.132	113.945	289.336
lumiN	1.371	0.140	1.523
lumiQ	0.570	0.087	0.666
lumiR	0.018	0.009	0.027
lumiR.batch	0.003	0.005	0.008
lumiT	0.723	0.107	0.844
methylationCall	10.605	6.504	17.310
normalizeMethylation.quantile	0.360	0.090	0.452
normalizeMethylation.ssn	0.311	0.062	0.375
nuID2EntrezID	12.402	0.079	12.488
nuID2IlluminaID	5.635	0.256	5.909
nuID2RefSeqID	24.249	0.072	24.321
nuID2probeID	5.263	0.228	5.504
nuID2targetID	6.195	0.281	6.500
pairs-methods	1.739	0.246	2.005
plot-methods	3.133	0.232	4.052
plotCDF	0.326	0.049	1.134
plotColorBias1D	0.515	0.071	0.604
plotColorBias2D	0.363	0.031	0.405
plotControlData	0.368	0.023	0.404
plotDensity	0.188	0.020	0.209
plotGammaFit	11.561	7.699	19.400
plotHousekeepingGene	0.277	0.018	0.296
plotSampleRelation	2.308	0.044	2.354
plotStringencyGene	0.378	0.020	0.400
plotVST	0.763	0.113	0.884
probeID2nuID	6.027	0.269	6.313
produceGEOPlatformFile	0.003	0.005	0.008
produceGEOSubmissionFile	0.061	0.009	0.070
produceMethylationGEOSubmissionFile	0.094	0.010	0.104
seq2id	0.004	0.008	0.013
targetID2nuID	6.972	0.308	7.288
vst	1.323	0.135	1.460

Summary

Command output