BioC 3.0: CHECK report for lumi on perceval

Package: lumi

Version: 2.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.18.0.tar.gz

StartedAt: 2015-04-10 03:11:32 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 03:27:04 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 932.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/lumi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘2.18.0’
* 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 ... [53s/57s] OK
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.2Mb
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [360s/372s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
lumiMethyStatus    126.940 16.111 144.076
getNuIDMappingInfo  30.331  0.236  30.614
nuID2EntrezID       22.810  0.110  22.993
nuID2RefSeqID       22.139  0.148  27.188
plotGammaFit        11.380  1.096  12.589
getChipInfo         10.263  0.614  11.227
methylationCall      7.800  1.001   8.829
nuID2targetID        8.079  0.245   8.399
nuID2IlluminaID      7.479  0.270   9.460
probeID2nuID         7.332  0.263   7.690
nuID2probeID         7.112  0.251   7.387
targetID2nuID        7.035  0.255   7.320
gammaFitEM           7.119  0.036   7.219
MAplot-methods       7.031  0.062   7.982
* 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
  ‘/Users/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	2.791	0.063	3.232
MAplot-methods	7.031	0.062	7.982
addAnnotationInfo	0.069	0.004	0.073
addControlData2lumi	0	0	0
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	2.976	0.032	3.212
adjColorBias.ssn	1.483	0.015	1.539
bgAdjust	0.082	0.006	0.088
bgAdjustMethylation	0.269	0.011	0.280
boxplot-MethyLumiM-methods	0.790	0.022	0.844
boxplot-methods	0.877	0.012	0.963
boxplotColorBias	0.991	0.023	1.108
density-methods	0.104	0.010	0.121
detectOutlier	0.132	0.013	0.152
detectionCall	0.192	0.018	0.235
estimateBeta	0.161	0.012	0.225
estimateIntensity	1.159	0.022	1.201
estimateLumiCV	0.145	0.018	0.171
estimateM	1.588	0.032	1.638
estimateMethylationBG	0.275	0.005	0.279
example.lumi	0.093	0.010	0.103
example.lumiMethy	0.070	0.007	0.077
example.methyTitration	0.208	0.017	0.226
gammaFitEM	7.119	0.036	7.219
getChipInfo	10.263	0.614	11.227
getControlData	0.004	0.001	0.005
getControlProbe	0.004	0.000	0.004
getControlType	0.004	0.001	0.004
getNuIDMappingInfo	30.331	0.236	30.614
hist-methods	0.129	0.017	0.154
id2seq	0.002	0.000	0.002
inverseVST	0.918	0.045	0.962
is.nuID	0.002	0.001	0.002
lumiB	0.088	0.009	0.096
lumiExpresso	0.441	0.037	0.478
lumiMethyB	0.091	0.008	0.100
lumiMethyC	3.737	0.138	3.927
lumiMethyN	0.096	0.008	0.104
lumiMethyStatus	126.940	16.111	144.076
lumiN	0.678	0.031	0.723
lumiQ	0.391	0.026	0.448
lumiR	0.000	0.000	0.001
lumiR.batch	0.001	0.001	0.001
lumiT	0.514	0.038	0.626
methylationCall	7.800	1.001	8.829
normalizeMethylation.quantile	0.268	0.028	0.297
normalizeMethylation.ssn	0.265	0.015	0.280
nuID2EntrezID	22.810	0.110	22.993
nuID2IlluminaID	7.479	0.270	9.460
nuID2RefSeqID	22.139	0.148	27.188
nuID2probeID	7.112	0.251	7.387
nuID2targetID	8.079	0.245	8.399
pairs-methods	1.151	0.083	1.661
plot-methods	3.036	0.100	3.311
plotCDF	0.161	0.012	0.185
plotColorBias1D	0.493	0.036	0.610
plotColorBias2D	0.384	0.009	0.417
plotControlData	0.004	0.001	0.005
plotDensity	0.139	0.011	0.159
plotGammaFit	11.380	1.096	12.589
plotHousekeepingGene	0.004	0.001	0.005
plotSampleRelation	1.019	0.022	1.125
plotStringencyGene	0.004	0.001	0.004
plotVST	0.435	0.025	0.519
probeID2nuID	7.332	0.263	7.690
produceGEOPlatformFile	0.001	0.000	0.001
produceGEOSubmissionFile	0.001	0.001	0.000
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.002	0.001	0.002
targetID2nuID	7.035	0.255	7.320
vst	0.506	0.031	0.553