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: 2017-10-18 00:25:23 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:31:20 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 356.9 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 3.4.2 (2017-09-28)
* 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 53.244  0.004  53.289
plotGammaFit     5.288  0.004   5.302
getChipInfo      4.436  0.096   5.668
* 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	2.084	0.056	2.143
MAplot-methods	4.676	0.008	4.685
addAnnotationInfo	0.072	0.000	0.069
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	0.984	0.008	0.989
adjColorBias.ssn	0.920	0.020	0.941
bgAdjust	0.076	0.000	0.075
bgAdjustMethylation	0.192	0.000	0.193
boxplot-MethyLumiM-methods	0.652	0.004	0.661
boxplot-methods	0.1	0.0	0.1
boxplotColorBias	0.12	0.00	0.12
density-methods	0.080	0.004	0.082
detectOutlier	0.088	0.000	0.089
detectionCall	0.172	0.000	0.171
estimateBeta	0.152	0.000	0.151
estimateIntensity	0.184	0.000	0.185
estimateLumiCV	0.088	0.000	0.091
estimateM	0.504	0.000	0.506
estimateMethylationBG	0.144	0.000	0.142
example.lumi	0.076	0.000	0.074
example.lumiMethy	0.048	0.004	0.054
example.methyTitration	0.708	0.004	0.713
gammaFitEM	4.432	0.004	4.531
getChipInfo	4.436	0.096	5.668
getControlData	0.000	0.000	0.001
getControlProbe	0.004	0.000	0.001
getControlType	0.000	0.000	0.001
getNuIDMappingInfo	1.004	0.016	1.019
hist-methods	0.152	0.000	0.152
id2seq	0.000	0.000	0.001
inverseVST	0.692	0.000	0.695
is.nuID	0.000	0.000	0.002
lumiB	0.132	0.000	0.136
lumiExpresso	0.544	0.000	0.556
lumiMethyB	0.060	0.000	0.057
lumiMethyC	1.624	0.004	1.628
lumiMethyN	0.076	0.000	0.083
lumiMethyStatus	53.244	0.004	53.289
lumiN	0.576	0.000	0.582
lumiQ	0.272	0.004	0.276
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.340	0.004	0.348
methylationCall	3.500	0.000	3.503
normalizeMethylation.quantile	0.16	0.00	0.16
normalizeMethylation.ssn	0.152	0.000	0.152
nuID2EntrezID	1.036	0.000	1.038
nuID2IlluminaID	4.232	0.004	4.238
nuID2RefSeqID	0.932	0.000	0.934
nuID2probeID	3.284	0.004	3.290
nuID2targetID	3.880	0.008	3.893
pairs-methods	0.9	0.0	0.9
plot-methods	1.988	0.008	1.996
plotCDF	0.132	0.004	0.136
plotColorBias1D	0.212	0.004	0.216
plotColorBias2D	0.184	0.000	0.183
plotControlData	0.004	0.000	0.001
plotDensity	0.100	0.004	0.105
plotGammaFit	5.288	0.004	5.302
plotHousekeepingGene	0.000	0.000	0.001
plotSampleRelation	0.596	0.032	0.629
plotStringencyGene	0.000	0.000	0.002
plotVST	0.276	0.016	0.294
probeID2nuID	2.944	0.004	2.949
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.000	0.000	0.001
targetID2nuID	3.260	0.000	3.263
vst	0.264	0.000	0.263