BioC 3.2: CHECK report for lumi on linux1.bioconductor.org

Package: lumi

Version: 2.22.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.22.0.tar.gz

StartedAt: 2015-10-27 05:10:49 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:17:35 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 405.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 4

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/lumi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘2.22.0’
* 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 ... [25s/25s] 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 ‘/home/biocbuild/bbs-3.2-bioc/meat/lumi.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  9.1Mb
  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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [164s/164s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 81.167  0.016  81.300
nuID2IlluminaID  5.486  0.008   5.505
MAplot-methods   5.438  0.020   5.464
methylationCall  5.441  0.004   5.446
getChipInfo      5.050  0.084   5.166
targetID2nuID    5.119  0.000   5.122
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
** 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
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	2.043	0.048	2.091
MAplot-methods	5.438	0.020	5.464
addAnnotationInfo	0.052	0.000	0.052
addControlData2lumi	0	0	0
addNuID2lumi	0	0	0
adjColorBias.quantile	1.536	0.000	1.537
adjColorBias.ssn	0.67	0.00	0.67
bgAdjust	0.098	0.008	0.106
bgAdjustMethylation	0.724	0.000	0.725
boxplot-MethyLumiM-methods	1.294	0.008	1.302
boxplot-methods	0.143	0.000	0.142
boxplotColorBias	0.261	0.004	0.265
density-methods	0.082	0.000	0.082
detectOutlier	0.134	0.004	0.138
detectionCall	0.221	0.000	0.221
estimateBeta	0.142	0.004	0.145
estimateIntensity	0.201	0.000	0.204
estimateLumiCV	0.668	0.000	0.668
estimateM	0.796	0.000	0.796
estimateMethylationBG	0.158	0.000	0.159
example.lumi	0.072	0.000	0.072
example.lumiMethy	0.047	0.000	0.047
example.methyTitration	0.160	0.000	0.161
gammaFitEM	4.840	0.000	4.846
getChipInfo	5.050	0.084	5.166
getControlData	0.000	0.000	0.001
getControlProbe	0.000	0.000	0.001
getControlType	0.000	0.000	0.001
getNuIDMappingInfo	1.388	0.008	1.405
hist-methods	0.153	0.004	0.156
id2seq	0.002	0.000	0.002
inverseVST	0.566	0.008	0.574
is.nuID	0.001	0.000	0.002
lumiB	0.072	0.004	0.076
lumiExpresso	0.299	0.000	0.299
lumiMethyB	0.066	0.000	0.066
lumiMethyC	1.859	0.000	1.858
lumiMethyN	0.075	0.000	0.076
lumiMethyStatus	81.167	0.016	81.300
lumiN	0.693	0.000	0.698
lumiQ	0.345	0.000	0.346
lumiR	0.001	0.000	0.001
lumiR.batch	0.000	0.000	0.001
lumiT	0.532	0.004	0.536
methylationCall	5.441	0.004	5.446
normalizeMethylation.quantile	0.16	0.00	0.16
normalizeMethylation.ssn	0.147	0.000	0.148
nuID2EntrezID	1.157	0.000	1.157
nuID2IlluminaID	5.486	0.008	5.505
nuID2RefSeqID	1.585	0.004	1.589
nuID2probeID	4.375	0.032	4.410
nuID2targetID	3.438	0.004	3.444
pairs-methods	0.930	0.004	0.935
plot-methods	2.562	0.004	2.570
plotCDF	0.129	0.004	0.133
plotColorBias1D	0.201	0.000	0.202
plotColorBias2D	0.168	0.004	0.172
plotControlData	0.001	0.000	0.002
plotDensity	0.096	0.004	0.099
plotGammaFit	4.117	0.000	4.125
plotHousekeepingGene	0.002	0.000	0.001
plotSampleRelation	0.549	0.008	0.557
plotStringencyGene	0.001	0.000	0.001
plotVST	0.316	0.004	0.320
probeID2nuID	3.464	0.008	3.475
produceGEOPlatformFile	0.000	0.000	0.001
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0.001	0.000	0.001
targetID2nuID	5.119	0.000	5.122
vst	0.306	0.004	0.309