BioC 3.6: CHECK report for lumi on veracruz1

Package: lumi

Version: 2.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.29.0.tar.gz

StartedAt: 2017-08-16 04:58:56 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 05:05:40 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 403.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 3

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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_2.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.29.0’
* 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 ... WARNING
Package unavailable to check Rd xrefs: ‘hdrcde’
Missing link or links in documentation object 'lumiN.Rd':
  ‘[vsn]{vsn}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 58.636  3.491  64.111
plotGammaFit     5.097  0.126   5.345
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.6-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	2.336	0.055	2.464
MAplot-methods	3.578	0.038	3.717
addAnnotationInfo	0.051	0.003	0.054
addControlData2lumi	0.001	0.000	0.000
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	1.606	0.038	1.692
adjColorBias.ssn	0.643	0.016	0.675
bgAdjust	0.084	0.004	0.096
bgAdjustMethylation	0.298	0.007	0.310
boxplot-MethyLumiM-methods	0.617	0.015	0.651
boxplot-methods	0.092	0.006	0.098
boxplotColorBias	0.690	0.014	0.721
density-methods	0.090	0.006	0.098
detectOutlier	0.087	0.009	0.098
detectionCall	0.195	0.012	0.209
estimateBeta	0.184	0.008	0.195
estimateIntensity	0.163	0.008	0.174
estimateLumiCV	0.103	0.007	0.110
estimateM	0.562	0.022	0.601
estimateMethylationBG	0.200	0.003	0.208
example.lumi	0.072	0.004	0.081
example.lumiMethy	0.051	0.002	0.060
example.methyTitration	0.180	0.009	0.195
gammaFitEM	3.429	0.268	3.806
getChipInfo	4.079	0.177	4.485
getControlData	0.003	0.000	0.003
getControlProbe	0.002	0.001	0.002
getControlType	0.002	0.000	0.003
getNuIDMappingInfo	1.198	0.044	1.271
hist-methods	0.108	0.006	0.116
id2seq	0.001	0.000	0.000
inverseVST	0.755	0.010	0.795
is.nuID	0.001	0.000	0.002
lumiB	0.144	0.005	0.152
lumiExpresso	0.526	0.011	0.550
lumiMethyB	0.052	0.003	0.055
lumiMethyC	2.042	0.041	2.142
lumiMethyN	0.078	0.004	0.082
lumiMethyStatus	58.636	3.491	64.111
lumiN	0.570	0.014	0.599
lumiQ	0.252	0.010	0.275
lumiR	0.000	0.001	0.000
lumiR.batch	0.001	0.000	0.000
lumiT	0.331	0.011	0.356
methylationCall	3.772	0.204	4.101
normalizeMethylation.quantile	0.156	0.009	0.174
normalizeMethylation.ssn	0.226	0.005	0.243
nuID2EntrezID	1.085	0.032	1.158
nuID2IlluminaID	3.807	0.062	3.954
nuID2RefSeqID	1.659	0.022	1.725
nuID2probeID	3.472	0.048	3.599
nuID2targetID	3.237	0.046	3.382
pairs-methods	0.870	0.037	0.918
plot-methods	1.773	0.025	1.859
plotCDF	0.114	0.006	0.122
plotColorBias1D	0.256	0.005	0.271
plotColorBias2D	0.260	0.004	0.274
plotControlData	0.003	0.000	0.003
plotDensity	0.142	0.004	0.149
plotGammaFit	5.097	0.126	5.345
plotHousekeepingGene	0.001	0.001	0.001
plotSampleRelation	0.814	0.009	0.850
plotStringencyGene	0.002	0.000	0.002
plotVST	0.266	0.010	0.293
probeID2nuID	3.403	0.046	3.599
produceGEOPlatformFile	0.001	0.000	0.000
produceGEOSubmissionFile	0.001	0.000	0.001
produceMethylationGEOSubmissionFile	0.001	0.001	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	3.786	0.050	3.939
vst	0.265	0.008	0.280