BioC 3.2: CHECK report for lumi on oaxaca

Package: lumi

Version: 2.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.22.0.tar.gz

StartedAt: 2015-10-27 05:09:52 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:17:33 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 461.0 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_2.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/lumi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.22.0’
* 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 ... [23s/23s] 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-3.2-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 : .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
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 ... [164s/166s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 73.033  5.038  78.202
getChipInfo      5.008  0.273   6.258
* 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-3.2-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	2.397	0.073	2.471
MAplot-methods	4.587	0.050	4.648
addAnnotationInfo	0.074	0.005	0.079
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	1.595	0.047	1.668
adjColorBias.ssn	0.693	0.018	0.718
bgAdjust	0.087	0.004	0.092
bgAdjustMethylation	0.613	0.005	0.619
boxplot-MethyLumiM-methods	1.188	0.013	1.251
boxplot-methods	0.125	0.009	0.135
boxplotColorBias	0.261	0.014	0.275
density-methods	0.109	0.012	0.121
detectOutlier	0.109	0.012	0.122
detectionCall	0.192	0.019	0.211
estimateBeta	0.119	0.004	0.124
estimateIntensity	0.166	0.006	0.172
estimateLumiCV	0.532	0.009	0.542
estimateM	0.705	0.015	0.721
estimateMethylationBG	0.242	0.002	0.244
example.lumi	0.099	0.009	0.108
example.lumiMethy	0.064	0.002	0.066
example.methyTitration	0.226	0.012	0.237
gammaFitEM	4.338	0.367	4.758
getChipInfo	5.008	0.273	6.258
getControlData	0.003	0.000	0.009
getControlProbe	0.002	0.000	0.003
getControlType	0.002	0.000	0.003
getNuIDMappingInfo	1.977	0.062	2.070
hist-methods	0.127	0.014	0.143
id2seq	0.002	0.000	0.001
inverseVST	0.628	0.023	0.652
is.nuID	0.001	0.000	0.001
lumiB	0.095	0.010	0.104
lumiExpresso	0.327	0.020	0.346
lumiMethyB	0.136	0.006	0.141
lumiMethyC	2.369	0.067	2.447
lumiMethyN	0.088	0.003	0.091
lumiMethyStatus	73.033	5.038	78.202
lumiN	0.563	0.016	0.983
lumiQ	0.297	0.010	0.312
lumiR	0	0	0
lumiR.batch	0.001	0.000	0.001
lumiT	0.406	0.012	0.426
methylationCall	4.245	0.230	4.478
normalizeMethylation.quantile	0.154	0.006	0.160
normalizeMethylation.ssn	0.225	0.004	0.229
nuID2EntrezID	1.634	0.033	1.668
nuID2IlluminaID	3.898	0.103	4.002
nuID2RefSeqID	1.090	0.025	1.114
nuID2probeID	4.069	0.110	4.181
nuID2targetID	3.909	0.101	4.012
pairs-methods	1.049	0.039	1.092
plot-methods	2.073	0.028	2.124
plotCDF	0.151	0.008	0.160
plotColorBias1D	0.889	0.010	0.903
plotColorBias2D	0.324	0.005	0.330
plotControlData	0.002	0.000	0.003
plotDensity	0.133	0.009	0.144
plotGammaFit	4.245	0.253	4.504
plotHousekeepingGene	0.002	0.000	0.002
plotSampleRelation	0.851	0.026	0.910
plotStringencyGene	0.002	0.000	0.002
plotVST	0.364	0.010	0.380
probeID2nuID	4.105	0.112	4.219
produceGEOPlatformFile	0	0	0
produceGEOSubmissionFile	0.000	0.000	0.001
produceMethylationGEOSubmissionFile	0.001	0.001	0.001
seq2id	0.001	0.000	0.002
targetID2nuID	4.444	0.111	4.561
vst	0.861	0.015	0.892