BioC 2.12: CHECK report for lumi on george2

Package: lumi

Version: 2.11.6

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.11.6.tar.gz

StartedAt: 2013-03-25 02:47:50 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 03:09:25 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 1294.9 seconds

RetCode: 0

Status: WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* 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 ‘2.11.6’
* 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 ... [73s/74s] OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    7.9Mb
* 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NB: .First.lib is obsolete and will not be used in R 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [11m/11m] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
lumiMethyStatus       298.559  0.156 306.562
nuID2RefSeqID          41.243  0.024  41.766
getNuIDMappingInfo     38.870  0.044  40.118
nuID2EntrezID          36.662  0.036  37.680
methylationCall        17.221  0.072  18.510
gammaFitEM             16.353  0.012  16.632
plotGammaFit           16.041  0.008  16.423
getChipInfo            14.081  0.244  14.798
nuID2IlluminaID        11.561  0.024  12.177
targetID2nuID          10.385  0.036  10.450
nuID2targetID          10.173  0.024  10.504
nuID2probeID           10.004  0.024  10.055
probeID2nuID            9.548  0.052   9.797
LumiBatch-class         8.013  0.092   8.347
adjColorBias.quantile   7.461  0.020   7.487
MAplot-methods          7.020  0.060   7.530
plot-methods            5.572  0.040   6.211
lumiMethyC              4.464  0.128   5.505
* 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
  ‘/home/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	8.013	0.092	8.347
MAplot-methods	7.02	0.06	7.53
addAnnotationInfo	0.104	0.012	0.116
addControlData2lumi	0.004	0.000	0.006
addNuID2lumi	0.016	0.000	0.017
adjColorBias.quantile	7.461	0.020	7.487
adjColorBias.ssn	2.348	0.012	2.360
bgAdjust	0.108	0.004	0.114
bgAdjustMethylation	1.616	0.012	1.628
boxplot-MethyLumiM-methods	2.204	0.004	2.210
boxplot-methods	0.336	0.004	0.342
boxplotColorBias	3.152	0.000	3.152
density-methods	0.168	0.004	0.173
detectOutlier	0.205	0.008	0.209
detectionCall	0.228	0.012	0.241
estimateBeta	1.324	0.008	1.334
estimateIntensity	0.444	0.000	0.444
estimateLumiCV	0.156	0.012	0.169
estimateM	2.048	0.024	2.076
estimateMethylationBG	0.424	0.000	0.426
example.lumi	0.124	0.008	0.132
example.lumiMethy	0.092	0.000	0.092
example.methyTitration	0.252	0.012	0.264
gammaFitEM	16.353	0.012	16.632
getChipInfo	14.081	0.244	14.798
getControlData	1.748	0.060	1.805
getControlProbe	0.192	0.004	0.197
getControlType	0.168	0.008	0.177
getNuIDMappingInfo	38.870	0.044	40.118
hist-methods	0.296	0.028	0.326
id2seq	0.012	0.000	0.011
inverseVST	2.021	0.016	2.141
is.nuID	0.092	0.004	0.100
lumiB	0.248	0.004	0.254
lumiExpresso	2.392	0.080	2.736
lumiMethyB	0.104	0.000	0.102
lumiMethyC	4.464	0.128	5.505
lumiMethyN	0.140	0.004	0.197
lumiMethyStatus	298.559	0.156	306.562
lumiN	1.284	0.004	1.297
lumiQ	1.816	0.008	1.907
lumiR	0.008	0.000	0.007
lumiR.batch	0.004	0.000	0.006
lumiT	0.748	0.004	0.859
methylationCall	17.221	0.072	18.510
normalizeMethylation.quantile	0.428	0.012	0.438
normalizeMethylation.ssn	0.536	0.008	0.545
nuID2EntrezID	36.662	0.036	37.680
nuID2IlluminaID	11.561	0.024	12.177
nuID2RefSeqID	41.243	0.024	41.766
nuID2probeID	10.004	0.024	10.055
nuID2targetID	10.173	0.024	10.504
pairs-methods	2.596	0.020	2.619
plot-methods	5.572	0.040	6.211
plotCDF	0.212	0.008	0.222
plotColorBias1D	0.428	0.008	0.435
plotColorBias2D	0.292	0.008	0.302
plotControlData	0.328	0.000	0.327
plotDensity	0.196	0.004	0.200
plotGammaFit	16.041	0.008	16.423
plotHousekeepingGene	0.312	0.008	0.352
plotSampleRelation	1.420	0.004	1.552
plotStringencyGene	0.312	0.004	0.315
plotVST	0.776	0.012	0.788
probeID2nuID	9.548	0.052	9.797
produceGEOPlatformFile	0.004	0.000	0.006
produceGEOSubmissionFile	0.104	0.000	0.105
produceMethylationGEOSubmissionFile	0.008	0.000	0.008
seq2id	0.012	0.000	0.009
targetID2nuID	10.385	0.036	10.450
vst	1.432	0.008	1.440

Summary

Command output