BioC 3.0: CHECK report for lumi on zin1

Package: lumi

Version: 2.18.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.18.0.tar.gz

StartedAt: 2015-04-10 01:30:45 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:39:45 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 540.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/lumi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘2.18.0’
* 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 ... [34s/37s] OK
* checking installed package size ... NOTE
  installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.4Mb
* 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
* 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’
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’
combine,LumiBatch-LumiBatch: no visible global function definition for
  ‘protocolData<-’
combine,LumiBatch-LumiBatch: no visible global function definition for
  ‘protocolData’
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’
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 ... NOTE
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
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [191s/195s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lumiMethyStatus    88.545  0.000  89.220
getNuIDMappingInfo  7.292  0.032   7.490
nuID2RefSeqID       6.785  0.000   6.819
nuID2EntrezID       6.540  0.016   6.570
methylationCall     5.357  0.008   5.549
plotGammaFit        5.280  0.004   5.297
getChipInfo         5.112  0.136   6.160
* 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

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-3.0-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	2.061	0.032	2.095
MAplot-methods	4.644	0.008	4.660
addAnnotationInfo	0.056	0.000	0.055
addControlData2lumi	0.004	0.000	0.000
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	1.852	0.008	1.874
adjColorBias.ssn	0.948	0.012	0.963
bgAdjust	0.076	0.004	0.081
bgAdjustMethylation	0.228	0.000	0.229
boxplot-MethyLumiM-methods	0.960	0.000	0.962
boxplot-methods	0.108	0.000	0.106
boxplotColorBias	0.576	0.000	0.578
density-methods	0.100	0.000	0.099
detectOutlier	0.100	0.000	0.101
detectionCall	0.540	0.000	0.541
estimateBeta	0.120	0.000	0.118
estimateIntensity	0.176	0.000	0.176
estimateLumiCV	0.112	0.004	0.116
estimateM	0.604	0.004	0.608
estimateMethylationBG	0.552	0.000	0.553
example.lumi	0.072	0.004	0.079
example.lumiMethy	0.056	0.000	0.056
example.methyTitration	0.180	0.004	0.184
gammaFitEM	4.673	0.000	4.766
getChipInfo	5.112	0.136	6.160
getControlData	0.004	0.000	0.004
getControlProbe	0.004	0.000	0.004
getControlType	0.004	0.000	0.003
getNuIDMappingInfo	7.292	0.032	7.490
hist-methods	0.12	0.00	0.12
id2seq	0.000	0.000	0.001
inverseVST	0.576	0.008	0.601
is.nuID	0.000	0.000	0.001
lumiB	0.084	0.004	0.086
lumiExpresso	0.333	0.012	0.362
lumiMethyB	0.056	0.000	0.057
lumiMethyC	1.964	0.000	1.968
lumiMethyN	0.080	0.000	0.108
lumiMethyStatus	88.545	0.000	89.220
lumiN	0.624	0.012	0.698
lumiQ	0.296	0.012	0.312
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.456	0.000	0.460
methylationCall	5.357	0.008	5.549
normalizeMethylation.quantile	0.212	0.004	0.217
normalizeMethylation.ssn	0.236	0.000	0.237
nuID2EntrezID	6.540	0.016	6.570
nuID2IlluminaID	4.344	0.020	4.521
nuID2RefSeqID	6.785	0.000	6.819
nuID2probeID	3.936	0.016	3.973
nuID2targetID	4.268	0.016	4.342
pairs-methods	1.084	0.008	1.275
plot-methods	2.268	0.028	2.329
plotCDF	0.200	0.008	0.210
plotColorBias1D	0.360	0.004	0.367
plotColorBias2D	0.28	0.00	0.28
plotControlData	0.004	0.000	0.005
plotDensity	0.133	0.004	0.137
plotGammaFit	5.280	0.004	5.297
plotHousekeepingGene	0.004	0.000	0.003
plotSampleRelation	0.820	0.008	0.831
plotStringencyGene	0.000	0.000	0.003
plotVST	0.376	0.000	0.377
probeID2nuID	3.788	0.020	3.815
produceGEOPlatformFile	0.004	0.000	0.001
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0.004	0.000	0.000
seq2id	0.000	0.000	0.001
targetID2nuID	3.684	0.012	3.710
vst	0.364	0.000	0.365