BioC 3.2: CHECK report for lumi on perceval

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 09:26:27 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 09:35:22 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 535.0 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 Patched (2015-10-08 r69496)
* 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 ‘2.22.0’
* 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 ... [32s/32s] 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’
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’
MAplot,ExpressionSet : .local: no visible global function definition
  for ‘rowMin’
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 ... [208s/209s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 92.426 12.739 105.169
MAplot-methods   6.737  0.043   6.786
getChipInfo      6.251  0.407   7.167
plotGammaFit     5.509  0.921   6.430
methylationCall  5.222  0.020   5.245
nuID2IlluminaID  4.987  0.159   5.147
probeID2nuID     4.920  0.181   5.102
targetID2nuID    4.899  0.140   5.039
nuID2targetID    4.900  0.137   5.037
nuID2probeID     4.860  0.151   5.011
* 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	2.382	0.072	2.455
MAplot-methods	6.737	0.043	6.786
addAnnotationInfo	0.071	0.004	0.077
addControlData2lumi	0.000	0.001	0.001
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	1.937	0.021	1.992
adjColorBias.ssn	1.232	0.009	1.243
bgAdjust	0.099	0.005	0.104
bgAdjustMethylation	0.268	0.007	0.276
boxplot-MethyLumiM-methods	1.338	0.021	1.360
boxplot-methods	0.135	0.006	0.142
boxplotColorBias	0.818	0.021	0.839
density-methods	0.111	0.008	0.119
detectOutlier	0.122	0.009	0.132
detectionCall	0.191	0.011	0.204
estimateBeta	0.142	0.009	0.152
estimateIntensity	0.197	0.011	0.209
estimateLumiCV	0.126	0.006	0.133
estimateM	0.716	0.017	0.733
estimateMethylationBG	0.257	0.003	0.259
example.lumi	0.100	0.007	0.106
example.lumiMethy	0.626	0.004	0.630
example.methyTitration	0.218	0.010	0.228
gammaFitEM	4.937	0.012	4.969
getChipInfo	6.251	0.407	7.167
getControlData	0.003	0.001	0.003
getControlProbe	0.002	0.000	0.002
getControlType	0.002	0.001	0.002
getNuIDMappingInfo	2.362	0.102	2.476
hist-methods	0.139	0.008	0.149
id2seq	0.001	0.000	0.002
inverseVST	0.615	0.019	0.635
is.nuID	0.001	0.000	0.002
lumiB	0.131	0.004	0.136
lumiExpresso	0.335	0.024	0.360
lumiMethyB	0.071	0.004	0.076
lumiMethyC	2.706	0.045	2.756
lumiMethyN	0.101	0.004	0.106
lumiMethyStatus	92.426	12.739	105.169
lumiN	0.628	0.018	0.646
lumiQ	0.311	0.023	0.338
lumiR	0.001	0.001	0.001
lumiR.batch	0.001	0.000	0.001
lumiT	0.451	0.028	0.487
methylationCall	5.222	0.020	5.245
normalizeMethylation.quantile	0.242	0.012	0.254
normalizeMethylation.ssn	0.273	0.006	0.277
nuID2EntrezID	2.235	0.052	2.287
nuID2IlluminaID	4.987	0.159	5.147
nuID2RefSeqID	1.722	0.041	1.763
nuID2probeID	4.860	0.151	5.011
nuID2targetID	4.900	0.137	5.037
pairs-methods	1.133	0.063	1.200
plot-methods	2.763	0.067	2.870
plotCDF	0.169	0.014	0.184
plotColorBias1D	1.182	0.038	1.222
plotColorBias2D	0.387	0.006	0.395
plotControlData	0.003	0.000	0.004
plotDensity	0.145	0.012	0.157
plotGammaFit	5.509	0.921	6.430
plotHousekeepingGene	0.002	0.000	0.002
plotSampleRelation	0.970	0.036	1.007
plotStringencyGene	0.002	0.000	0.002
plotVST	0.409	0.025	0.438
probeID2nuID	4.920	0.181	5.102
produceGEOPlatformFile	0.001	0.000	0.001
produceGEOSubmissionFile	0.001	0.000	0.000
produceMethylationGEOSubmissionFile	0.001	0.000	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	4.899	0.140	5.039
vst	1.007	0.027	1.033