BioC 3.5: CHECK report for lumi on malbec2

Package: lumi

Version: 2.28.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.28.0.tar.gz

StartedAt: 2017-08-16 00:14:13 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:20:18 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 364.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 2

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/lumi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-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 ‘2.28.0’
* 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 54.028  0.008  54.077
plotGammaFit     5.216  0.004   5.223
gammaFitEM       5.008  0.000   5.013
getChipInfo      4.780  0.100   5.369
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  ‘/home/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	2.320	0.032	2.354
MAplot-methods	4.144	0.024	4.168
addAnnotationInfo	0.044	0.008	0.054
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	1.512	0.016	1.525
adjColorBias.ssn	0.488	0.004	0.494
bgAdjust	0.076	0.016	0.089
bgAdjustMethylation	0.216	0.000	0.215
boxplot-MethyLumiM-methods	1.128	0.000	1.129
boxplot-methods	0.088	0.004	0.091
boxplotColorBias	0.152	0.000	0.153
density-methods	0.100	0.004	0.102
detectOutlier	0.076	0.016	0.094
detectionCall	0.160	0.024	0.186
estimateBeta	0.152	0.000	0.151
estimateIntensity	0.188	0.000	0.185
estimateLumiCV	0.088	0.004	0.092
estimateM	0.496	0.004	0.501
estimateMethylationBG	0.160	0.000	0.161
example.lumi	0.072	0.016	0.087
example.lumiMethy	0.056	0.000	0.058
example.methyTitration	0.204	0.004	0.206
gammaFitEM	5.008	0.000	5.013
getChipInfo	4.780	0.100	5.369
getControlData	0.000	0.000	0.001
getControlProbe	0.004	0.000	0.001
getControlType	0.000	0.000	0.001
getNuIDMappingInfo	1.392	0.016	1.410
hist-methods	0.108	0.012	0.118
id2seq	0.000	0.000	0.001
inverseVST	0.624	0.016	0.644
is.nuID	0.000	0.000	0.001
lumiB	0.168	0.016	0.184
lumiExpresso	0.476	0.024	0.502
lumiMethyB	0.060	0.000	0.062
lumiMethyC	1.772	0.016	1.791
lumiMethyN	0.088	0.000	0.091
lumiMethyStatus	54.028	0.008	54.077
lumiN	0.556	0.012	0.571
lumiQ	0.256	0.008	0.266
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.320	0.004	0.324
methylationCall	3.404	0.000	3.404
normalizeMethylation.quantile	0.152	0.000	0.152
normalizeMethylation.ssn	0.168	0.000	0.167
nuID2EntrezID	0.948	0.008	0.956
nuID2IlluminaID	3.608	0.008	3.618
nuID2RefSeqID	1.660	0.004	1.667
nuID2probeID	3.188	0.008	3.199
nuID2targetID	3.276	0.008	3.286
pairs-methods	0.924	0.016	0.941
plot-methods	1.904	0.020	1.925
plotCDF	0.192	0.000	0.193
plotColorBias1D	0.300	0.000	0.302
plotColorBias2D	0.200	0.000	0.199
plotControlData	0.004	0.000	0.001
plotDensity	0.188	0.000	0.190
plotGammaFit	5.216	0.004	5.223
plotHousekeepingGene	0.000	0.000	0.001
plotSampleRelation	0.596	0.008	0.604
plotStringencyGene	0.000	0.000	0.001
plotVST	0.284	0.012	0.295
probeID2nuID	3.148	0.008	3.158
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.004	0.000	0.001
targetID2nuID	3.184	0.008	3.196
vst	0.232	0.000	0.235