BioC 2.12: CHECK report for lumi on lamb2

Package: lumi

Version: 2.11.5

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.11.5.tar.gz

StartedAt: 2013-01-16 04:00:10 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 04:13:55 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 824.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘2.11.5’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    7.8Mb
* 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 ... OK
* 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)
  Docs: function(x, ..., smoothScatter = FALSE, logMode = TRUE, subset
                 = 5000, fold = 2, dotColor = 1, main = NULL)
  Argument names in code not in docs:
    highlight highlightColor
  Mismatches in argument names:
    Position: 8 Code: highlight Docs: main

* 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 ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
lumiMethyStatus    198.153  0.108 198.758
nuID2RefSeqID       30.470  0.016  30.584
getNuIDMappingInfo  22.741  0.036  22.786
nuID2EntrezID       20.569  0.016  20.692
methylationCall     10.533  0.012  10.620
plotGammaFit        10.504  0.000  10.510
getChipInfo          9.997  0.152  10.490
gammaFitEM           9.973  0.004  10.012
nuID2IlluminaID      7.877  0.012   7.939
probeID2nuID         6.656  0.012   6.670
MAplot-methods       6.600  0.048   6.694
nuID2targetID        6.544  0.004   6.557
nuID2probeID         6.460  0.012   6.509
targetID2nuID        6.152  0.028   6.203
* 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 2 notes.
See
  ‘/loc/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’

* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	3.508	0.048	3.563
MAplot-methods	6.600	0.048	6.694
addAnnotationInfo	0.080	0.008	0.086
addControlData2lumi	0.012	0.000	0.011
addNuID2lumi	0.020	0.000	0.021
adjColorBias.quantile	4.601	0.036	4.668
adjColorBias.ssn	1.676	0.004	1.690
bgAdjust	0.100	0.004	0.109
bgAdjustMethylation	1.096	0.004	1.111
boxplot-MethyLumiM-methods	1.408	0.004	1.418
boxplot-methods	0.268	0.004	0.274
boxplotColorBias	1.236	0.008	1.251
density-methods	0.124	0.000	0.123
detectOutlier	0.132	0.000	0.137
detectionCall	0.184	0.020	0.206
estimateBeta	0.856	0.004	0.869
estimateIntensity	0.328	0.004	0.336
estimateLumiCV	0.116	0.004	0.123
estimateM	1.356	0.012	1.382
estimateMethylationBG	0.292	0.000	0.296
example.lumi	0.092	0.000	0.093
example.lumiMethy	0.080	0.000	0.079
example.methyTitration	0.212	0.000	0.215
gammaFitEM	9.973	0.004	10.012
getChipInfo	9.997	0.152	10.490
getControlData	1.848	0.040	1.894
getControlProbe	0.148	0.008	0.155
getControlType	0.148	0.004	0.154
getNuIDMappingInfo	22.741	0.036	22.786
hist-methods	0.212	0.004	0.217
id2seq	0.076	0.000	0.077
inverseVST	2.368	0.012	2.396
is.nuID	0.024	0.000	0.026
lumiB	0.12	0.00	0.12
lumiExpresso	0.428	0.000	0.430
lumiMethyB	0.064	0.000	0.063
lumiMethyC	3.288	0.012	3.302
lumiMethyN	0.116	0.004	0.124
lumiMethyStatus	198.153	0.108	198.758
lumiN	1.612	0.012	1.635
lumiQ	0.360	0.004	0.369
lumiR	0.020	0.000	0.021
lumiR.batch	0.02	0.00	0.02
lumiT	0.548	0.004	0.553
methylationCall	10.533	0.012	10.620
normalizeMethylation.quantile	1.040	0.004	1.055
normalizeMethylation.ssn	0.360	0.004	0.366
nuID2EntrezID	20.569	0.016	20.692
nuID2IlluminaID	7.877	0.012	7.939
nuID2RefSeqID	30.470	0.016	30.584
nuID2probeID	6.460	0.012	6.509
nuID2targetID	6.544	0.004	6.557
pairs-methods	1.488	0.020	1.509
plot-methods	3.077	0.012	3.088
plotCDF	0.272	0.012	0.282
plotColorBias1D	0.644	0.004	0.652
plotColorBias2D	0.316	0.004	0.317
plotControlData	0.212	0.000	0.214
plotDensity	0.144	0.004	0.146
plotGammaFit	10.504	0.000	10.510
plotHousekeepingGene	0.216	0.004	0.217
plotSampleRelation	1.065	0.000	1.066
plotStringencyGene	0.212	0.004	0.216
plotVST	0.512	0.020	0.533
probeID2nuID	6.656	0.012	6.670
produceGEOPlatformFile	0.084	0.000	0.086
produceGEOSubmissionFile	0.092	0.000	0.095
produceMethylationGEOSubmissionFile	0.08	0.00	0.08
seq2id	0.008	0.000	0.005
targetID2nuID	6.152	0.028	6.203
vst	1.525	0.000	1.529

Summary

Command output