BioC 3.4: CHECK report for lumi on malbec1

Package: lumi

Version: 2.26.4

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.26.4.tar.gz

StartedAt: 2017-04-14 23:31:32 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:37:24 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 352.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.26.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/lumi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘2.26.4’
* 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: ‘bigmemoryExtras’
* 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’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 55.156  0.032  55.240
getChipInfo      5.296  0.124   5.544
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-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	1.648	0.024	1.676
MAplot-methods	4.636	0.012	4.651
addAnnotationInfo	0.056	0.000	0.060
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	0.888	0.008	0.897
adjColorBias.ssn	0.448	0.008	0.456
bgAdjust	0.548	0.000	0.548
bgAdjustMethylation	0.160	0.000	0.159
boxplot-MethyLumiM-methods	0.5	0.0	0.5
boxplot-methods	0.584	0.000	0.584
boxplotColorBias	0.148	0.000	0.149
density-methods	0.084	0.000	0.087
detectOutlier	0.084	0.000	0.087
detectionCall	0.144	0.000	0.144
estimateBeta	0.096	0.000	0.097
estimateIntensity	0.560	0.004	0.567
estimateLumiCV	0.096	0.000	0.093
estimateM	0.464	0.004	0.467
estimateMethylationBG	0.176	0.008	0.183
example.lumi	0.068	0.004	0.073
example.lumiMethy	0.056	0.000	0.056
example.methyTitration	0.176	0.000	0.175
gammaFitEM	4.512	0.004	4.521
getChipInfo	5.296	0.124	5.544
getControlData	0.004	0.000	0.002
getControlProbe	0.000	0.000	0.001
getControlType	0.004	0.000	0.002
getNuIDMappingInfo	1.116	0.016	1.140
hist-methods	0.116	0.000	0.115
id2seq	0.004	0.000	0.001
inverseVST	0.452	0.004	0.464
is.nuID	0.004	0.000	0.001
lumiB	0.084	0.004	0.089
lumiExpresso	0.316	0.004	0.330
lumiMethyB	0.060	0.000	0.061
lumiMethyC	1.500	0.004	1.509
lumiMethyN	0.092	0.000	0.096
lumiMethyStatus	55.156	0.032	55.240
lumiN	0.440	0.008	0.450
lumiQ	0.236	0.012	0.248
lumiR	0.000	0.000	0.001
lumiR.batch	0	0	0
lumiT	0.344	0.016	0.361
methylationCall	3.520	0.000	3.527
normalizeMethylation.quantile	0.160	0.000	0.159
normalizeMethylation.ssn	0.180	0.000	0.179
nuID2EntrezID	1.784	0.008	1.795
nuID2IlluminaID	3.824	0.004	3.829
nuID2RefSeqID	1.152	0.008	1.164
nuID2probeID	4.092	0.004	4.100
nuID2targetID	3.536	0.012	3.551
pairs-methods	0.776	0.016	0.791
plot-methods	1.808	0.004	1.812
plotCDF	0.184	0.000	0.184
plotColorBias1D	0.296	0.000	0.296
plotColorBias2D	0.184	0.000	0.184
plotControlData	0.000	0.000	0.001
plotDensity	0.120	0.004	0.125
plotGammaFit	4.144	0.000	4.146
plotHousekeepingGene	0.004	0.000	0.001
plotSampleRelation	0.516	0.004	0.520
plotStringencyGene	0.000	0.000	0.001
plotVST	0.288	0.008	0.298
probeID2nuID	3.248	0.004	3.253
produceGEOPlatformFile	0.004	0.000	0.000
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.004	0.000	0.001
targetID2nuID	3.672	0.000	3.673
vst	0.260	0.004	0.264