BioC 3.5: CHECK report for lumi on tokay2

Package: lumi

Version: 2.28.0

Command: rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.28.0.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.28.0.tar.gz

StartedAt: 2017-10-18 00:59:24 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:10:01 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 637.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 2

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### Running command:
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###   rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.28.0.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/lumi.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Packages unavailable to check Rd xrefs: 'bigmemoryExtras', '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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 57.72   0.02   57.73
getChipInfo      6.50   0.28   21.82
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 54.50    0.0   54.50
getChipInfo      5.11    0.1    5.21
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/lumi.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'lumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lumi' as lumi_2.28.0.zip
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	2.09	0.16	2.25
MAplot-methods	4.27	0.00	4.26
addAnnotationInfo	0.07	0.00	0.06
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	1.52	0.00	1.51
adjColorBias.ssn	1.11	0.00	1.11
bgAdjust	0.14	0.02	0.16
bgAdjustMethylation	0.84	0.00	0.84
boxplot-MethyLumiM-methods	1.17	0.00	1.17
boxplot-methods	0.13	0.00	0.13
boxplotColorBias	0.12	0.03	0.15
density-methods	0.11	0.01	0.13
detectOutlier	0.10	0.00	0.09
detectionCall	0.17	0.02	0.19
estimateBeta	0.17	0.00	0.17
estimateIntensity	0.56	0.00	0.56
estimateLumiCV	0.13	0.00	0.13
estimateM	1.06	0.01	1.08
estimateMethylationBG	0.13	0.04	0.15
example.lumi	0.07	0.00	0.08
example.lumiMethy	0.05	0.00	0.04
example.methyTitration	0.18	0.01	0.21
gammaFitEM	3.46	0.02	3.51
getChipInfo	6.50	0.28	21.82
getControlData	0	0	0
getControlProbe	0	0	0
getControlType	0	0	0
getNuIDMappingInfo	1.46	0.03	2.25
hist-methods	0.15	0.00	0.16
id2seq	0	0	0
inverseVST	0.81	0.05	0.86
is.nuID	0	0	0
lumiB	0.13	0.00	0.12
lumiExpresso	0.49	0.01	0.50
lumiMethyB	0.08	0.00	0.08
lumiMethyC	2.00	0.02	2.01
lumiMethyN	0.09	0.01	0.11
lumiMethyStatus	57.72	0.02	57.73
lumiN	0.69	0.06	1.35
lumiQ	0.42	0.00	0.42
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.44	0.00	0.43
methylationCall	3.8	0.0	3.8
normalizeMethylation.quantile	0.16	0.02	0.17
normalizeMethylation.ssn	0.17	0.00	0.17
nuID2EntrezID	0.90	0.01	0.93
nuID2IlluminaID	3.72	0.00	3.71
nuID2RefSeqID	0.92	0.03	0.96
nuID2probeID	2.54	0.02	2.54
nuID2targetID	2.59	0.03	2.63
pairs-methods	1.25	0.00	1.25
plot-methods	1.66	0.02	1.67
plotCDF	0.15	0.00	0.15
plotColorBias1D	0.22	0.00	0.22
plotColorBias2D	0.19	0.00	0.19
plotControlData	0	0	0
plotDensity	0.11	0.00	0.11
plotGammaFit	3.08	0.01	3.09
plotHousekeepingGene	0.01	0.00	0.02
plotSampleRelation	0.63	0.02	0.64
plotStringencyGene	0	0	0
plotVST	0.37	0.03	0.41
probeID2nuID	3.84	0.01	3.86
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	3.20	0.04	3.24
vst	0.47	0.00	0.46

name	user	system	elapsed
LumiBatch-class	2.58	0.00	2.58
MAplot-methods	4.13	0.01	4.15
addAnnotationInfo	0.05	0.00	0.05
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	1.34	0.03	1.37
adjColorBias.ssn	1.18	0.00	1.19
bgAdjust	0.08	0.00	0.07
bgAdjustMethylation	0.22	0.02	0.24
boxplot-MethyLumiM-methods	1.36	0.00	1.36
boxplot-methods	0.09	0.00	0.09
boxplotColorBias	0.27	0.00	0.27
density-methods	0.11	0.03	0.14
detectOutlier	0.72	0.00	0.72
detectionCall	0.19	0.00	0.18
estimateBeta	0.17	0.00	0.18
estimateIntensity	0.2	0.0	0.2
estimateLumiCV	0.13	0.00	0.12
estimateM	0.68	0.00	0.69
estimateMethylationBG	0.14	0.00	0.14
example.lumi	0.08	0.00	0.08
example.lumiMethy	0.08	0.00	0.08
example.methyTitration	0.19	0.00	0.19
gammaFitEM	3.81	0.06	3.96
getChipInfo	5.11	0.10	5.21
getControlData	0	0	0
getControlProbe	0	0	0
getControlType	0	0	0
getNuIDMappingInfo	1.18	0.00	1.19
hist-methods	0.11	0.00	0.11
id2seq	0	0	0
inverseVST	0.72	0.00	0.72
is.nuID	0	0	0
lumiB	0.18	0.00	0.19
lumiExpresso	0.47	0.00	0.47
lumiMethyB	0.07	0.00	0.06
lumiMethyC	2.20	0.05	2.25
lumiMethyN	0.11	0.00	0.11
lumiMethyStatus	54.5	0.0	54.5
lumiN	0.47	0.02	0.50
lumiQ	0.26	0.01	0.28
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.36	0.00	0.35
methylationCall	3.31	0.00	3.32
normalizeMethylation.quantile	0.12	0.02	0.14
normalizeMethylation.ssn	0.15	0.00	0.14
nuID2EntrezID	0.90	0.01	0.92
nuID2IlluminaID	3.77	0.00	3.77
nuID2RefSeqID	1.03	0.02	1.04
nuID2probeID	2.78	0.00	2.78
nuID2targetID	2.92	0.00	2.93
pairs-methods	0.92	0.03	0.95
plot-methods	1.96	0.00	1.95
plotCDF	0.23	0.00	0.24
plotColorBias1D	0.42	0.02	0.43
plotColorBias2D	0.24	0.01	0.25
plotControlData	0	0	0
plotDensity	0.18	0.02	0.21
plotGammaFit	3.99	0.00	3.98
plotHousekeepingGene	0	0	0
plotSampleRelation	0.64	0.00	0.64
plotStringencyGene	0	0	0
plotVST	0.28	0.01	0.30
probeID2nuID	2.61	0.02	2.62
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	2.81	0.00	2.81
vst	0.25	0.00	0.25