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 03:08:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:18:36 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 606.2 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 --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) (2019-03-18 r76245)
* 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 65.325 14.375  79.703
getChipInfo      6.930  0.611   7.631
plotGammaFit     6.036  0.910   6.947
MAplot-methods   5.507  0.140   5.647
nuID2targetID    5.498  0.135   5.632
nuID2IlluminaID  5.229  0.173   5.402
targetID2nuID    4.901  0.109   5.011
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	2.307	0.170	2.477
MAplot-methods	5.507	0.140	5.647
addAnnotationInfo	0.076	0.010	0.087
addControlData2lumi	0.001	0.000	0.000
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	1.124	0.177	1.302
adjColorBias.ssn	0.574	0.077	0.652
bgAdjust	0.093	0.009	0.102
bgAdjustMethylation	0.247	0.045	0.294
boxplot-MethyLumiM-methods	0.683	0.051	0.735
boxplot-methods	0.131	0.013	0.144
boxplotColorBias	0.213	0.051	0.264
density-methods	0.103	0.010	0.113
detectOutlier	0.129	0.014	0.144
detectionCall	0.179	0.013	0.193
estimateBeta	0.304	0.029	0.333
estimateIntensity	0.336	0.029	0.366
estimateLumiCV	0.135	0.012	0.147
estimateM	1.733	0.042	1.776
estimateMethylationBG	0.156	0.017	0.174
example.lumi	0.096	0.014	0.110
example.lumiMethy	0.054	0.008	0.062
example.methyTitration	0.167	0.016	0.182
gammaFitEM	3.508	0.992	4.502
getChipInfo	6.930	0.611	7.631
getControlData	0.003	0.001	0.003
getControlProbe	0.001	0.000	0.002
getControlType	0.001	0.001	0.003
getNuIDMappingInfo	1.877	0.120	2.006
hist-methods	0.115	0.010	0.124
id2seq	0.002	0.000	0.002
inverseVST	0.801	0.068	0.869
is.nuID	0.001	0.001	0.001
lumiB	0.123	0.010	0.133
lumiExpresso	0.382	0.047	0.427
lumiMethyB	0.073	0.007	0.079
lumiMethyC	1.751	0.165	1.919
lumiMethyN	0.115	0.008	0.122
lumiMethyStatus	65.325	14.375	79.703
lumiN	0.475	0.064	0.539
lumiQ	0.316	0.029	0.346
lumiR	0.000	0.001	0.001
lumiR.batch	0	0	0
lumiT	0.461	0.056	0.518
methylationCall	3.491	0.840	4.357
normalizeMethylation.quantile	0.214	0.045	0.258
normalizeMethylation.ssn	0.210	0.027	0.237
nuID2EntrezID	1.251	0.062	1.313
nuID2IlluminaID	5.229	0.173	5.402
nuID2RefSeqID	1.319	0.064	1.384
nuID2probeID	4.543	0.112	4.656
nuID2targetID	5.498	0.135	5.632
pairs-methods	0.956	0.109	1.074
plot-methods	2.510	0.103	2.618
plotCDF	0.188	0.021	0.210
plotColorBias1D	0.248	0.015	0.265
plotColorBias2D	0.276	0.009	0.286
plotControlData	0.002	0.000	0.002
plotDensity	0.114	0.007	0.122
plotGammaFit	6.036	0.910	6.947
plotHousekeepingGene	0.002	0.001	0.002
plotSampleRelation	1.083	0.039	1.123
plotStringencyGene	0.002	0.000	0.002
plotVST	0.369	0.024	0.397
probeID2nuID	4.847	0.120	4.968
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0.000	0.001	0.001
produceMethylationGEOSubmissionFile	0.001	0.000	0.000
seq2id	0.001	0.000	0.001
targetID2nuID	4.901	0.109	5.011
vst	0.452	0.028	0.481