Package: lumi

Version: 2.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.30.0.tar.gz

StartedAt: 2018-04-12 05:41:01 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:48:01 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 419.2 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_2.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘2.30.0’
* 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 59.880  2.680  63.900
getChipInfo      5.112  0.214   5.477
* 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	2.175	0.022	2.234
MAplot-methods	4.002	0.043	4.133
addAnnotationInfo	0.045	0.004	0.049
addControlData2lumi	0	0	0
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	0.968	0.030	1.008
adjColorBias.ssn	0.828	0.011	0.845
bgAdjust	0.066	0.004	0.072
bgAdjustMethylation	0.198	0.006	0.206
boxplot-MethyLumiM-methods	0.914	0.015	0.945
boxplot-methods	0.093	0.005	0.099
boxplotColorBias	0.150	0.012	0.162
density-methods	0.083	0.004	0.092
detectOutlier	0.090	0.006	0.101
detectionCall	0.149	0.009	0.159
estimateBeta	0.170	0.005	0.180
estimateIntensity	0.624	0.006	0.651
estimateLumiCV	0.107	0.005	0.120
estimateM	0.569	0.017	0.591
estimateMethylationBG	0.147	0.003	0.155
example.lumi	0.080	0.004	0.089
example.lumiMethy	0.054	0.002	0.056
example.methyTitration	0.162	0.007	0.169
gammaFitEM	3.430	0.240	3.727
getChipInfo	5.112	0.214	5.477
getControlData	0.002	0.000	0.003
getControlProbe	0.002	0.000	0.003
getControlType	0.002	0.000	0.002
getNuIDMappingInfo	1.904	0.078	2.024
hist-methods	0.113	0.007	0.124
id2seq	0.002	0.000	0.001
inverseVST	0.731	0.022	0.770
is.nuID	0.001	0.000	0.001
lumiB	0.137	0.005	0.144
lumiExpresso	0.527	0.015	0.552
lumiMethyB	0.060	0.004	0.066
lumiMethyC	1.505	0.030	1.563
lumiMethyN	0.078	0.004	0.082
lumiMethyStatus	59.88	2.68	63.90
lumiN	0.568	0.017	0.601
lumiQ	0.261	0.011	0.275
lumiR	0.000	0.000	0.001
lumiR.batch	0	0	0
lumiT	0.325	0.013	0.348
methylationCall	3.704	0.127	3.937
normalizeMethylation.quantile	0.172	0.010	0.184
normalizeMethylation.ssn	0.629	0.012	0.656
nuID2EntrezID	1.149	0.022	1.202
nuID2IlluminaID	4.387	0.074	4.547
nuID2RefSeqID	1.869	0.026	1.940
nuID2probeID	3.596	0.050	3.709
nuID2targetID	3.616	0.047	3.742
pairs-methods	1.289	0.040	1.347
plot-methods	1.892	0.027	1.952
plotCDF	0.126	0.009	0.138
plotColorBias1D	0.189	0.007	0.201
plotColorBias2D	0.278	0.005	0.291
plotControlData	0.002	0.001	0.002
plotDensity	0.113	0.005	0.124
plotGammaFit	3.253	0.172	3.486
plotHousekeepingGene	0.002	0.001	0.002
plotSampleRelation	0.800	0.013	0.828
plotStringencyGene	0.002	0.000	0.002
plotVST	0.287	0.024	0.324
probeID2nuID	3.424	0.052	3.547
produceGEOPlatformFile	0.000	0.001	0.000
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0.001	0.000	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	4.428	0.054	4.609
vst	0.240	0.009	0.266