BioC 3.3: CHECK report for lumi on morelia

Package: lumi

Version: 2.23.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.23.0.tar.gz

StartedAt: 2015-10-22 07:46:35 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 07:52:09 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 334.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 4

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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_2.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘2.23.0’
* 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 ... [20s/20s] 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 ‘/Users/biocbuild/bbs-3.3-bioc/meat/lumi.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    4.9Mb
* 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’
MAplot,ExpressionSet: no visible global function definition for
  ‘rowMin’
asBigMatrix,ExpressionSet: no visible global function definition for
  ‘assayDataElementNames’
asBigMatrix,ExpressionSet: no visible global function definition for
  ‘assayDataElement’
asBigMatrix,ExpressionSet: no visible global function definition for
  ‘assayDataElement<-’
asBigMatrix,ExpressionSet: no visible global function definition for
  ‘AnnotatedDataFrame’
asBigMatrix,ExpressionSet: 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: no visible global function definition for
  ‘description’
boxplot,ExpressionSet: no visible global function definition for
  ‘rowMin’
boxplot,MethyLumiM: 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: 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: 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’
Undefined global functions or variables:
  AnnotatedDataFrame assayDataElement assayDataElement<-
  assayDataElementNames assayDataElementReplace assayDataValidMembers
  description fData fData<- keys notes<- protocolData protocolData<-
  rowMin storageMode<-
* 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
Package unavailable to check Rd xrefs: ‘bigmemoryExtras’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [128s/129s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 59.018  5.117  64.199
* 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
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
** 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
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	1.490	0.056	1.546
MAplot-methods	3.738	0.043	3.786
addAnnotationInfo	0.045	0.002	0.047
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	1.115	0.028	1.159
adjColorBias.ssn	0.635	0.017	0.654
bgAdjust	0.094	0.004	0.097
bgAdjustMethylation	0.568	0.010	0.578
boxplot-MethyLumiM-methods	0.759	0.010	0.769
boxplot-methods	0.076	0.007	0.083
boxplotColorBias	0.187	0.015	0.202
density-methods	0.082	0.004	0.086
detectOutlier	0.073	0.004	0.078
detectionCall	0.140	0.006	0.146
estimateBeta	0.081	0.003	0.084
estimateIntensity	0.119	0.005	0.126
estimateLumiCV	0.124	0.005	0.130
estimateM	0.779	0.013	0.793
estimateMethylationBG	0.144	0.004	0.147
example.lumi	0.075	0.008	0.082
example.lumiMethy	0.061	0.001	0.063
example.methyTitration	0.219	0.011	0.230
gammaFitEM	3.435	0.276	3.750
getChipInfo	3.859	0.195	4.482
getControlData	0.001	0.000	0.001
getControlProbe	0.001	0.000	0.002
getControlType	0.001	0.000	0.001
getNuIDMappingInfo	1.286	0.046	1.353
hist-methods	0.087	0.005	0.093
id2seq	0.001	0.000	0.001
inverseVST	0.348	0.013	0.362
is.nuID	0.001	0.000	0.001
lumiB	0.062	0.003	0.064
lumiExpresso	0.193	0.007	0.201
lumiMethyB	0.065	0.003	0.069
lumiMethyC	1.538	0.027	1.568
lumiMethyN	0.072	0.001	0.073
lumiMethyStatus	59.018	5.117	64.199
lumiN	0.518	0.019	0.537
lumiQ	0.298	0.016	0.318
lumiR	0.001	0.000	0.000
lumiR.batch	0.001	0.000	0.001
lumiT	0.327	0.012	0.345
methylationCall	3.407	0.112	3.544
normalizeMethylation.quantile	0.148	0.004	0.152
normalizeMethylation.ssn	0.173	0.003	0.177
nuID2EntrezID	0.865	0.022	0.887
nuID2IlluminaID	3.531	0.097	3.632
nuID2RefSeqID	1.360	0.034	1.393
nuID2probeID	3.046	0.068	3.115
nuID2targetID	2.854	0.070	2.924
pairs-methods	0.777	0.032	0.928
plot-methods	1.719	0.034	1.774
plotCDF	0.192	0.008	0.201
plotColorBias1D	0.709	0.008	0.720
plotColorBias2D	0.294	0.004	0.299
plotControlData	0.001	0.001	0.001
plotDensity	0.087	0.003	0.091
plotGammaFit	4.092	0.501	4.596
plotHousekeepingGene	0.001	0.001	0.001
plotSampleRelation	0.784	0.009	0.795
plotStringencyGene	0.002	0.000	0.002
plotVST	0.345	0.017	0.366
probeID2nuID	3.056	0.078	3.136
produceGEOPlatformFile	0.001	0.000	0.000
produceGEOSubmissionFile	0.001	0.000	0.001
produceMethylationGEOSubmissionFile	0.001	0.000	0.001
seq2id	0.000	0.000	0.001
targetID2nuID	3.023	0.075	3.099
vst	0.619	0.019	0.638