BioC 3.5: CHECK report for lumi on toluca2

Package: lumi

Version: 2.27.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.27.3.tar.gz

StartedAt: 2017-04-23 05:58:40 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 06:06:29 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 468.8 seconds

RetCode: 0

Status: WARNINGS

CheckDir: lumi.Rcheck

Warnings: 2

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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_2.27.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.27.3’
* 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 ... OK
* 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 66.110  5.625  72.673
getChipInfo      6.005  0.232   6.326
nuID2IlluminaID  4.987  0.103   5.161
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/Users/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	2.891	0.077	3.041
MAplot-methods	4.483	0.052	4.653
addAnnotationInfo	0.061	0.004	0.066
addControlData2lumi	0.001	0.000	0.001
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	1.484	0.044	1.608
adjColorBias.ssn	1.200	0.011	1.338
bgAdjust	0.098	0.004	0.106
bgAdjustMethylation	0.343	0.009	0.359
boxplot-MethyLumiM-methods	1.372	0.018	1.422
boxplot-methods	0.110	0.007	0.116
boxplotColorBias	0.205	0.017	0.224
density-methods	0.112	0.007	0.121
detectOutlier	0.108	0.006	0.122
detectionCall	0.250	0.013	0.264
estimateBeta	0.198	0.005	0.210
estimateIntensity	0.227	0.006	0.237
estimateLumiCV	0.117	0.007	0.128
estimateM	2.723	0.055	2.806
estimateMethylationBG	0.247	0.020	0.268
example.lumi	0.090	0.005	0.096
example.lumiMethy	0.061	0.002	0.064
example.methyTitration	0.699	0.011	0.716
gammaFitEM	3.825	0.382	4.251
getChipInfo	6.005	0.232	6.326
getControlData	0.002	0.001	0.003
getControlProbe	0.002	0.000	0.002
getControlType	0.002	0.000	0.002
getNuIDMappingInfo	1.382	0.052	1.450
hist-methods	0.191	0.013	0.207
id2seq	0.002	0.000	0.001
inverseVST	0.873	0.016	0.895
is.nuID	0.001	0.000	0.002
lumiB	0.167	0.007	0.176
lumiExpresso	0.742	0.014	0.763
lumiMethyB	0.065	0.004	0.070
lumiMethyC	2.109	0.037	2.196
lumiMethyN	0.087	0.003	0.090
lumiMethyStatus	66.110	5.625	72.673
lumiN	0.661	0.025	0.694
lumiQ	0.324	0.021	0.352
lumiR	0.001	0.001	0.001
lumiR.batch	0.001	0.000	0.001
lumiT	0.375	0.014	0.401
methylationCall	4.226	0.275	4.687
normalizeMethylation.quantile	0.177	0.012	0.189
normalizeMethylation.ssn	0.228	0.008	0.238
nuID2EntrezID	1.451	0.049	1.519
nuID2IlluminaID	4.987	0.103	5.161
nuID2RefSeqID	1.916	0.037	1.970
nuID2probeID	4.333	0.079	4.442
nuID2targetID	4.234	0.085	4.377
pairs-methods	1.027	0.039	1.077
plot-methods	2.295	0.037	2.379
plotCDF	0.200	0.017	0.221
plotColorBias1D	0.334	0.007	0.346
plotColorBias2D	0.321	0.006	0.331
plotControlData	0.002	0.000	0.002
plotDensity	0.179	0.014	0.194
plotGammaFit	4.176	0.348	4.564
plotHousekeepingGene	0.002	0.000	0.002
plotSampleRelation	1.155	0.011	1.179
plotStringencyGene	0.001	0.000	0.002
plotVST	0.333	0.016	0.358
probeID2nuID	4.313	0.079	4.416
produceGEOPlatformFile	0.001	0.000	0.001
produceGEOSubmissionFile	0.001	0.000	0.000
produceMethylationGEOSubmissionFile	0.001	0.000	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	4.669	0.084	4.817
vst	0.247	0.006	0.254

BioC 3.5: CHECK report for lumi on toluca2

Summary

Command output