BioC 3.5: CHECK report for lumi on veracruz2

Package: lumi

Version: 2.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.28.0.tar.gz

StartedAt: 2017-10-18 05:27:11 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 05:33:30 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 378.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/lumi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.28.0’
* 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 ... OK
* checking installed package size ... OK
* 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 dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  ‘IRanges’ ‘bigmemoryExtras’
* 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘hdrcde’
* 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘IlluminaAnnotation.R’, ‘IlluminaAnnotation.pdf’, ‘lumi.R’,
    ‘lumi.pdf’, ‘lumi_VST_evaluation.R’, ‘lumi_VST_evaluation.pdf’,
    ‘methylationAnalysis.R’, ‘methylationAnalysis.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 56.109  1.656  59.474
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	2.391	0.072	2.510
MAplot-methods	3.551	0.050	3.686
addAnnotationInfo	0.052	0.004	0.056
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	1.480	0.038	1.570
adjColorBias.ssn	0.423	0.008	0.449
bgAdjust	0.072	0.004	0.078
bgAdjustMethylation	0.216	0.008	0.228
boxplot-MethyLumiM-methods	0.588	0.015	0.614
boxplot-methods	0.089	0.005	0.099
boxplotColorBias	0.591	0.015	0.626
density-methods	0.080	0.005	0.089
detectOutlier	0.105	0.008	0.125
detectionCall	0.170	0.013	0.188
estimateBeta	0.169	0.007	0.187
estimateIntensity	0.199	0.008	0.211
estimateLumiCV	0.103	0.013	0.121
estimateM	0.542	0.016	0.577
estimateMethylationBG	0.633	0.007	0.649
example.lumi	0.073	0.004	0.080
example.lumiMethy	0.054	0.002	0.065
example.methyTitration	0.154	0.008	0.168
gammaFitEM	3.065	0.087	3.236
getChipInfo	4.348	0.186	4.702
getControlData	0.001	0.000	0.002
getControlProbe	0.002	0.000	0.001
getControlType	0.001	0.000	0.002
getNuIDMappingInfo	1.143	0.048	1.232
hist-methods	0.111	0.008	0.127
id2seq	0.001	0.000	0.002
inverseVST	0.811	0.014	0.867
is.nuID	0.002	0.000	0.001
lumiB	0.138	0.006	0.146
lumiExpresso	0.484	0.018	0.513
lumiMethyB	0.046	0.003	0.050
lumiMethyC	2.046	0.040	2.148
lumiMethyN	0.074	0.003	0.077
lumiMethyStatus	56.109	1.656	59.474
lumiN	0.469	0.012	0.499
lumiQ	0.234	0.009	0.252
lumiR	0.000	0.001	0.000
lumiR.batch	0	0	0
lumiT	0.301	0.011	0.330
methylationCall	3.774	0.095	3.994
normalizeMethylation.quantile	0.150	0.007	0.158
normalizeMethylation.ssn	0.145	0.006	0.156
nuID2EntrezID	1.153	0.026	1.232
nuID2IlluminaID	3.922	0.082	4.112
nuID2RefSeqID	1.701	0.043	1.798
nuID2probeID	3.242	0.056	3.401
nuID2targetID	3.188	0.056	3.328
pairs-methods	1.061	0.033	1.114
plot-methods	1.535	0.035	1.612
plotCDF	0.093	0.006	0.100
plotColorBias1D	0.159	0.007	0.175
plotColorBias2D	0.213	0.005	0.225
plotControlData	0.001	0.000	0.001
plotDensity	0.090	0.005	0.098
plotGammaFit	2.901	0.056	3.034
plotHousekeepingGene	0.001	0.000	0.001
plotSampleRelation	0.863	0.014	0.899
plotStringencyGene	0.001	0.001	0.002
plotVST	0.265	0.012	0.299
probeID2nuID	3.270	0.056	3.425
produceGEOPlatformFile	0.000	0.000	0.001
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0.001	0.000	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	3.408	0.057	3.574
vst	0.789	0.019	0.852