BioC 3.1: CHECK report for lumi on moscato2

Package: lumi

Version: 2.20.2

Command: rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.20.2.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.20.2.tar.gz

StartedAt: 2015-10-09 03:19:18 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:31:30 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 731.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 4

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### Running command:
###
###   rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.20.2.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.20.2.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/lumi.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '2.20.2'
* 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 ... WARNING
Found the following significant warnings:
  Warning: bad markup (extra space?) at lumiMethyR.Rd:18:16
  Warning: bad markup (extra space?) at lumiMethyR.Rd:19:28
  Warning: bad markup (extra space?) at lumiMethyR.Rd:20:13
See 'E:/biocbld/bbs-3.1-bioc/meat/lumi.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.3Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase'
A package should be listed in only one of these fields.
* 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 ':::' import not declared from: 'bigmemoryExtras'
'library' or 'require' call to 'vsn' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addAnnotationInfo: no visible global function definition for 'fData'
addAnnotationInfo: no visible global function definition for 'keys'
addAnnotationInfo: no visible global function definition for 'fData<-'
addNuID2lumi: no visible global function definition for 'notes<-'
adjColorBias.quantile: no visible global function definition for
  'assayDataElementNames'
adjColorBias.quantile: no visible global function definition for
  'storageMode<-'
adjColorBias.quantile: no visible global function definition for
  'assayDataElement'
adjColorBias.quantile: no visible global function definition for
  'assayDataElement<-'
adjColorBias.ssn: no visible global function definition for
  'assayDataElementNames'
adjColorBias.ssn: no visible global function definition for
  'storageMode<-'
adjColorBias.ssn: no visible global function definition for
  'assayDataElement'
adjColorBias.ssn: no visible global function definition for
  'assayDataElement<-'
bgAdjustMethylation: no visible global function definition for
  'assayDataElementNames'
boxplotColorBias: no visible global function definition for
  'assayDataElementNames'
boxplotColorBias: no visible global function definition for
  'assayDataElement'
colorBiasSummary: no visible global function definition for
  'assayDataElementNames'
colorBiasSummary: no visible global function definition for
  'assayDataElement'
detectionCall: no visible global function definition for
  'assayDataValidMembers'
detectionCall: no visible global function definition for
  'assayDataElement'
estimateBeta: no visible global function definition for
  'assayDataElementNames'
estimateBeta: no visible global function definition for
  'assayDataElement'
estimateBeta: no visible global function definition for
  'assayDataElement<-'
estimateIntensity: no visible global function definition for
  'assayDataElementNames'
estimateIntensity: no visible global function definition for
  'assayDataElement'
estimateIntensity: no visible global function definition for
  'assayDataElement<-'
estimateM: no visible global function definition for
  'assayDataElementNames'
estimateM: no visible global function definition for 'assayDataElement'
estimateM: no visible global function definition for
  'assayDataElement<-'
estimateMethylationBG: no visible global function definition for
  'assayDataElement'
estimateMethylationBG: no visible global function definition for
  'assayDataElementNames'
getChrInfo: no visible global function definition for 'fData'
importMethyIDAT: no visible global function definition for
  'assayDataElementNames'
importMethyIDAT: no visible global function definition for
  'assayDataElement'
lumiMethyB: no visible global function definition for
  'assayDataElement'
lumiMethyC: no visible global function definition for
  'assayDataElement'
lumiMethyN: no visible global function definition for
  'assayDataElement'
lumiQ: no visible global function definition for 'rowMin'
lumiR: no visible global function definition for 'notes<-'
normalizeMethylation.quantile: no visible global function definition
  for 'assayDataElementNames'
normalizeMethylation.quantile: no visible global function definition
  for 'storageMode<-'
normalizeMethylation.quantile: no visible global function definition
  for 'assayDataElement'
normalizeMethylation.quantile: no visible global function definition
  for 'assayDataElement<-'
normalizeMethylation.ssn: no visible global function definition for
  'assayDataElementNames'
normalizeMethylation.ssn: no visible global function definition for
  'storageMode<-'
normalizeMethylation.ssn: no visible global function definition for
  'assayDataElement'
normalizeMethylation.ssn: no visible global function definition for
  'assayDataElement<-'
plotCDF: no visible global function definition for 'rowMin'
plotColorBias1D: no visible global function definition for
  'assayDataElementNames'
plotColorBias1D: no visible global function definition for
  'assayDataElement'
plotColorBias2D: no visible global function definition for
  'assayDataElementNames'
plotColorBias2D: no visible global function definition for
  'assayDataElement'
plotControlData: no visible global function definition for
  'assayDataElement'
MAplot,ExpressionSet : .local: no visible global function definition
  for 'rowMin'
asBigMatrix,ExpressionSet : .local: no visible global function
  definition for 'assayDataElementNames'
asBigMatrix,ExpressionSet : .local: no visible global function
  definition for 'assayDataElement'
asBigMatrix,ExpressionSet : .local: no visible global function
  definition for 'assayDataElement<-'
asBigMatrix,ExpressionSet : .local: no visible global function
  definition for 'AnnotatedDataFrame'
asBigMatrix,ExpressionSet : .local: no visible global function
  definition for 'fData'
beadNum,ExpressionSet: no visible global function definition for
  'assayDataElementNames'
beadNum,ExpressionSet: no visible global function definition for
  'assayDataElement'
beadNum<-,ExpressionSet: no visible global function definition for
  'storageMode<-'
beadNum<-,ExpressionSet: no visible global function definition for
  'assayDataElementReplace'
boxplot,ExpressionSet : .local: no visible global function definition
  for 'description'
boxplot,ExpressionSet : .local: no visible global function definition
  for 'rowMin'
boxplot,MethyLumiM : .local: no visible global function definition for
  'description'
combine,LumiBatch-LumiBatch: no visible global function definition for
  'protocolData<-'
combine,LumiBatch-LumiBatch: no visible global function definition for
  'protocolData'
density,ExpressionSet : .local: no visible global function definition
  for 'rowMin'
detection,ExpressionSet: no visible global function definition for
  'assayDataElementNames'
detection,ExpressionSet: no visible global function definition for
  'assayDataElement'
detection<-,ExpressionSet: no visible global function definition for
  'storageMode<-'
detection<-,ExpressionSet: no visible global function definition for
  'assayDataElementReplace'
pairs,ExpressionSet : .local: no visible global function definition for
  'rowMin'
se.exprs,ExpressionSet: no visible global function definition for
  'assayDataElementNames'
se.exprs,ExpressionSet: no visible global function definition for
  'assayDataElement'
se.exprs<-,ExpressionSet: no visible global function definition for
  'storageMode<-'
se.exprs<-,ExpressionSet: no visible global function definition for
  'assayDataElementReplace'
* checking Rd files ... WARNING
prepare_Rd: getChrInfo.Rd:23-25: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:29-31: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:38-40: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:41-44: Dropping empty section \examples
prepare_Rd: importMethyIDAT.Rd:39-42: Dropping empty section \examples
prepare_Rd: bad markup (extra space?) at lumiMethyR.Rd:18:16
prepare_Rd: bad markup (extra space?) at lumiMethyR.Rd:19:28
prepare_Rd: bad markup (extra space?) at lumiMethyR.Rd:20:13
* 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 ... WARNING
Argument items with no description in Rd object 'lumiMethyR':
  'qcfile' 'sampleDescriptions' 'sep'

* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [187s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 91.69   0.01   91.70
getChipInfo      6.26   0.19   11.08
methylationCall  6.05   0.00    6.05
MAplot-methods   5.93   0.02    5.94
plotGammaFit     5.09   0.00    5.09
** running examples for arch 'x64' ... [189s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 91.09   0.00   91.12
plotGammaFit     6.54   0.02    6.56
methylationCall  6.38   0.00    6.38
MAplot-methods   6.22   0.02    6.24
probeID2nuID     6.02   0.03    6.05
targetID2nuID    5.46   0.00    5.46
gammaFitEM       5.43   0.00    5.42
getChipInfo      5.13   0.18    5.32
nuID2IlluminaID  5.25   0.01    5.52
nuID2targetID    5.18   0.00    5.17
nuID2probeID     5.03   0.02    5.04
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/lumi.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
Warning: bad markup (extra space?) at lumiMethyR.Rd:18:16
Warning: bad markup (extra space?) at lumiMethyR.Rd:19:28
Warning: bad markup (extra space?) at lumiMethyR.Rd:20:13
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'lumi' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'lumi' as lumi_2.20.2.zip
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	1.39	0.04	1.44
MAplot-methods	5.93	0.02	5.94
addAnnotationInfo	0.06	0.02	0.08
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	1.65	0.00	1.65
adjColorBias.ssn	0.95	0.00	0.95
bgAdjust	0.10	0.01	0.11
bgAdjustMethylation	0.67	0.00	0.67
boxplot-MethyLumiM-methods	1.57	0.02	1.59
boxplot-methods	0.13	0.00	0.13
boxplotColorBias	0.53	0.00	0.53
density-methods	0.09	0.01	0.11
detectOutlier	0.11	0.00	0.11
detectionCall	0.18	0.00	0.19
estimateBeta	0.14	0.00	0.14
estimateIntensity	0.19	0.00	0.19
estimateLumiCV	0.14	0.00	0.14
estimateM	1.26	0.00	1.26
estimateMethylationBG	0.19	0.00	0.19
example.lumi	0.09	0.00	0.09
example.lumiMethy	0.08	0.00	0.08
example.methyTitration	0.22	0.00	0.22
gammaFitEM	4.24	0.00	4.24
getChipInfo	6.26	0.19	11.08
getControlData	0	0	0
getControlProbe	0	0	0
getControlType	0	0	0
getNuIDMappingInfo	1.99	0.05	2.08
hist-methods	0.14	0.00	0.14
id2seq	0	0	0
inverseVST	0.54	0.00	0.55
is.nuID	0	0	0
lumiB	0.09	0.00	0.09
lumiExpresso	0.36	0.00	0.36
lumiMethyB	0.08	0.00	0.08
lumiMethyC	1.93	0.00	1.93
lumiMethyN	0.11	0.00	0.11
lumiMethyStatus	91.69	0.01	91.70
lumiN	0.78	0.00	0.78
lumiQ	0.70	0.02	0.71
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.62	0.01	0.83
methylationCall	6.05	0.00	6.05
normalizeMethylation.quantile	0.64	0.00	0.64
normalizeMethylation.ssn	0.22	0.00	0.22
nuID2EntrezID	1.67	0.02	1.70
nuID2IlluminaID	4.4	0.0	4.4
nuID2RefSeqID	1.70	0.00	1.71
nuID2probeID	4.09	0.00	4.09
nuID2targetID	4.13	0.01	4.15
pairs-methods	1.43	0.05	1.48
plot-methods	2.77	0.03	2.80
plotCDF	0.25	0.00	0.25
plotColorBias1D	0.29	0.00	0.29
plotColorBias2D	0.22	0.00	0.22
plotControlData	0.02	0.00	0.02
plotDensity	0.15	0.00	0.15
plotGammaFit	5.09	0.00	5.09
plotHousekeepingGene	0	0	0
plotSampleRelation	0.78	0.00	0.88
plotStringencyGene	0.02	0.00	0.01
plotVST	0.86	0.03	0.89
probeID2nuID	3.90	0.02	3.92
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	4.56	0.00	4.57
vst	0.34	0.00	0.35

name	user	system	elapsed
LumiBatch-class	2.25	0.01	2.27
MAplot-methods	6.22	0.02	6.24
addAnnotationInfo	0.06	0.00	0.06
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	1.46	0.00	1.47
adjColorBias.ssn	1.03	0.00	1.03
bgAdjust	0.07	0.01	0.08
bgAdjustMethylation	0.21	0.00	0.22
boxplot-MethyLumiM-methods	1.33	0.00	1.32
boxplot-methods	0.09	0.00	0.09
boxplotColorBias	0.21	0.00	0.22
density-methods	0.11	0.00	0.11
detectOutlier	0.14	0.00	0.14
detectionCall	0.16	0.00	0.15
estimateBeta	0.12	0.00	0.12
estimateIntensity	0.17	0.00	0.17
estimateLumiCV	0.12	0.00	0.12
estimateM	1.2	0.0	1.8
estimateMethylationBG	0.30	0.02	0.31
example.lumi	0.12	0.00	0.12
example.lumiMethy	0.10	0.01	0.11
example.methyTitration	0.31	0.00	0.32
gammaFitEM	5.43	0.00	5.42
getChipInfo	5.13	0.18	5.32
getControlData	0	0	0
getControlProbe	0	0	0
getControlType	0	0	0
getNuIDMappingInfo	2.24	0.00	2.25
hist-methods	0.13	0.00	0.12
id2seq	0	0	0
inverseVST	0.58	0.00	0.58
is.nuID	0	0	0
lumiB	0.08	0.00	0.08
lumiExpresso	0.31	0.00	0.31
lumiMethyB	0.09	0.01	0.11
lumiMethyC	2.09	0.00	2.09
lumiMethyN	0.13	0.02	0.14
lumiMethyStatus	91.09	0.00	91.12
lumiN	0.67	0.00	0.68
lumiQ	0.33	0.01	0.34
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.48	0.00	0.48
methylationCall	6.38	0.00	6.38
normalizeMethylation.quantile	0.20	0.00	0.21
normalizeMethylation.ssn	0.2	0.0	0.2
nuID2EntrezID	1.77	0.02	1.78
nuID2IlluminaID	5.25	0.01	5.52
nuID2RefSeqID	1.61	0.00	1.61
nuID2probeID	5.03	0.02	5.04
nuID2targetID	5.18	0.00	5.17
pairs-methods	1.34	0.00	1.35
plot-methods	2.62	0.01	2.63
plotCDF	0.23	0.00	0.24
plotColorBias1D	0.41	0.00	0.40
plotColorBias2D	0.20	0.00	0.21
plotControlData	0	0	0
plotDensity	0.23	0.00	0.23
plotGammaFit	6.54	0.02	6.56
plotHousekeepingGene	0	0	0
plotSampleRelation	1.07	0.00	1.07
plotStringencyGene	0	0	0
plotVST	0.69	0.02	0.70
probeID2nuID	6.02	0.03	6.05
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	5.46	0.00	5.46
vst	0.50	0.01	0.52