Package: lumi

Version: 2.35.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lumi_2.35.0.tar.gz

StartedAt: 2019-04-09 01:52:55 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:00:46 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 470.6 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 --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings lumi_2.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘2.35.0’
* 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 51.384  4.546  56.339
MAplot-methods   5.324  0.086   5.450
nuID2targetID    5.098  0.075   5.213
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/lumi.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL lumi
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘lumi’ ...
** R
** data
** inst
** byte-compile and prepare 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	1.682	0.094	1.794
MAplot-methods	5.324	0.086	5.450
addAnnotationInfo	0.071	0.005	0.078
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	0.945	0.080	1.035
adjColorBias.ssn	0.469	0.024	0.499
bgAdjust	0.097	0.006	0.105
bgAdjustMethylation	0.185	0.011	0.197
boxplot-MethyLumiM-methods	0.680	0.020	0.707
boxplot-methods	0.117	0.006	0.126
boxplotColorBias	0.867	0.025	0.896
density-methods	0.086	0.007	0.094
detectOutlier	0.115	0.014	0.131
detectionCall	0.170	0.013	0.185
estimateBeta	0.227	0.015	0.245
estimateIntensity	0.224	0.009	0.236
estimateLumiCV	0.118	0.007	0.130
estimateM	0.570	0.026	0.607
estimateMethylationBG	0.133	0.005	0.139
example.lumi	0.086	0.005	0.091
example.lumiMethy	0.066	0.003	0.069
example.methyTitration	0.222	0.009	0.231
gammaFitEM	3.570	0.316	3.915
getChipInfo	4.505	0.250	4.871
getControlData	0.001	0.000	0.002
getControlProbe	0.002	0.000	0.001
getControlType	0.001	0.000	0.001
getNuIDMappingInfo	1.178	0.055	1.239
hist-methods	0.128	0.006	0.134
id2seq	0.001	0.000	0.001
inverseVST	0.664	0.017	0.691
is.nuID	0.001	0.000	0.001
lumiB	0.092	0.005	0.099
lumiExpresso	0.293	0.012	0.307
lumiMethyB	0.059	0.004	0.062
lumiMethyC	1.139	0.049	1.197
lumiMethyN	0.102	0.003	0.105
lumiMethyStatus	51.384	4.546	56.339
lumiN	0.518	0.017	0.539
lumiQ	0.307	0.012	0.324
lumiR	0.001	0.000	0.000
lumiR.batch	0.000	0.001	0.000
lumiT	0.412	0.016	0.438
methylationCall	2.838	0.233	3.096
normalizeMethylation.quantile	0.202	0.019	0.226
normalizeMethylation.ssn	0.189	0.012	0.207
nuID2EntrezID	1.194	0.034	1.238
nuID2IlluminaID	4.204	0.105	4.344
nuID2RefSeqID	1.251	0.029	1.291
nuID2probeID	3.927	0.068	4.028
nuID2targetID	5.098	0.075	5.213
pairs-methods	1.022	0.066	1.096
plot-methods	2.633	0.044	2.702
plotCDF	0.173	0.009	0.185
plotColorBias1D	0.227	0.009	0.237
plotColorBias2D	0.233	0.007	0.241
plotControlData	0.001	0.000	0.001
plotDensity	0.137	0.006	0.144
plotGammaFit	3.605	0.296	3.943
plotHousekeepingGene	0.001	0.000	0.002
plotSampleRelation	1.913	0.016	1.950
plotStringencyGene	0.001	0.001	0.001
plotVST	0.360	0.015	0.392
probeID2nuID	4.184	0.064	4.291
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0.000	0.001	0.000
seq2id	0.001	0.000	0.001
targetID2nuID	4.093	0.073	4.194
vst	0.298	0.016	0.317