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: 2017-08-16 04:41:20 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:48:09 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 408.6 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 3.4.1 (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 ‘2.28.0’
* 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 59.635  2.496  64.031
plotGammaFit     5.870  0.113   6.177
getChipInfo      4.885  0.187   5.247
* 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	2.482	0.066	2.588
MAplot-methods	3.735	0.047	3.896
addAnnotationInfo	0.060	0.003	0.064
addControlData2lumi	0.001	0.000	0.000
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	1.666	0.041	1.749
adjColorBias.ssn	0.629	0.012	0.653
bgAdjust	0.089	0.004	0.095
bgAdjustMethylation	0.814	0.010	0.840
boxplot-MethyLumiM-methods	0.570	0.016	0.592
boxplot-methods	0.092	0.006	0.104
boxplotColorBias	0.642	0.014	0.674
density-methods	0.088	0.003	0.092
detectOutlier	0.090	0.006	0.099
detectionCall	0.170	0.010	0.195
estimateBeta	0.149	0.007	0.158
estimateIntensity	0.185	0.008	0.197
estimateLumiCV	0.088	0.006	0.096
estimateM	0.568	0.017	0.611
estimateMethylationBG	0.172	0.001	0.180
example.lumi	0.080	0.006	0.085
example.lumiMethy	0.056	0.001	0.058
example.methyTitration	0.190	0.008	0.201
gammaFitEM	3.053	0.210	3.365
getChipInfo	4.885	0.187	5.247
getControlData	0.002	0.000	0.003
getControlProbe	0.002	0.001	0.003
getControlType	0.002	0.000	0.002
getNuIDMappingInfo	1.407	0.051	1.488
hist-methods	0.118	0.005	0.135
id2seq	0.001	0.000	0.001
inverseVST	0.828	0.010	0.853
is.nuID	0.002	0.000	0.001
lumiB	0.130	0.005	0.138
lumiExpresso	0.517	0.010	0.532
lumiMethyB	0.125	0.006	0.132
lumiMethyC	2.135	0.041	2.239
lumiMethyN	0.075	0.003	0.077
lumiMethyStatus	59.635	2.496	64.031
lumiN	0.549	0.012	0.572
lumiQ	0.254	0.010	0.275
lumiR	0.000	0.000	0.001
lumiR.batch	0.001	0.000	0.001
lumiT	0.341	0.014	0.365
methylationCall	3.963	0.142	4.217
normalizeMethylation.quantile	0.152	0.006	0.164
normalizeMethylation.ssn	0.214	0.005	0.223
nuID2EntrezID	1.177	0.023	1.238
nuID2IlluminaID	4.152	0.070	4.339
nuID2RefSeqID	1.928	0.031	1.992
nuID2probeID	3.433	0.048	3.588
nuID2targetID	3.906	0.046	4.051
pairs-methods	0.693	0.031	0.747
plot-methods	1.716	0.026	1.797
plotCDF	0.127	0.007	0.137
plotColorBias1D	0.267	0.007	0.283
plotColorBias2D	0.270	0.005	0.284
plotControlData	0.001	0.000	0.001
plotDensity	0.103	0.005	0.113
plotGammaFit	5.870	0.113	6.177
plotHousekeepingGene	0.002	0.000	0.002
plotSampleRelation	0.804	0.010	0.842
plotStringencyGene	0.002	0.001	0.002
plotVST	0.300	0.012	0.322
probeID2nuID	3.261	0.044	3.394
produceGEOPlatformFile	0.000	0.000	0.001
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0.001	0.001	0.001
seq2id	0.001	0.000	0.002
targetID2nuID	3.371	0.045	3.510
vst	0.273	0.008	0.286