BioC 3.3: CHECK report for lumi on linux2.bioconductor.org

Package: lumi

Version: 2.23.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.23.0.tar.gz

StartedAt: 2015-10-27 05:19:27 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:25:49 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 381.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: lumi.Rcheck

Warnings: 4

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.23.0’
* 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 ... [21s/21s] 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-3.3-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: 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [157s/157s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 76.602  0.000  76.705
plotGammaFit     7.566  0.004   7.578
nuID2targetID    5.391  0.000   5.402
* 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-3.3-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	1.613	0.048	1.663
MAplot-methods	4.536	0.032	4.567
addAnnotationInfo	0.044	0.004	0.047
addControlData2lumi	0.001	0.000	0.000
addNuID2lumi	0.000	0.000	0.001
adjColorBias.quantile	0.951	0.004	0.956
adjColorBias.ssn	1.000	0.008	1.009
bgAdjust	0.109	0.000	0.110
bgAdjustMethylation	0.245	0.000	0.245
boxplot-MethyLumiM-methods	1.311	0.009	1.326
boxplot-methods	0.126	0.004	0.131
boxplotColorBias	0.226	0.004	0.229
density-methods	0.120	0.004	0.124
detectOutlier	0.133	0.003	0.137
detectionCall	0.208	0.008	0.216
estimateBeta	0.144	0.004	0.149
estimateIntensity	0.19	0.00	0.19
estimateLumiCV	0.139	0.008	0.147
estimateM	0.614	0.000	0.615
estimateMethylationBG	0.703	0.000	0.705
example.lumi	0.113	0.000	0.113
example.lumiMethy	0.071	0.003	0.076
example.methyTitration	0.161	0.000	0.161
gammaFitEM	3.824	0.004	3.831
getChipInfo	4.342	0.072	4.441
getControlData	0.003	0.000	0.002
getControlProbe	0.002	0.000	0.002
getControlType	0.002	0.000	0.002
getNuIDMappingInfo	1.179	0.008	1.190
hist-methods	0.103	0.000	0.103
id2seq	0.001	0.000	0.001
inverseVST	0.450	0.004	0.454
is.nuID	0.001	0.000	0.000
lumiB	0.697	0.000	0.697
lumiExpresso	0.282	0.000	0.282
lumiMethyB	0.074	0.000	0.074
lumiMethyC	1.526	0.008	1.538
lumiMethyN	0.097	0.000	0.097
lumiMethyStatus	76.602	0.000	76.705
lumiN	0.481	0.008	0.488
lumiQ	0.309	0.008	0.316
lumiR	0	0	0
lumiR.batch	0	0	0
lumiT	0.335	0.000	0.335
methylationCall	4.024	0.004	4.028
normalizeMethylation.quantile	0.139	0.000	0.138
normalizeMethylation.ssn	0.178	0.000	0.178
nuID2EntrezID	1.42	0.00	1.42
nuID2IlluminaID	4.676	0.008	4.689
nuID2RefSeqID	2.211	0.004	2.215
nuID2probeID	4.162	0.000	4.170
nuID2targetID	5.391	0.000	5.402
pairs-methods	1.154	0.012	1.168
plot-methods	2.282	0.024	2.432
plotCDF	0.201	0.012	0.213
plotColorBias1D	0.358	0.000	0.359
plotColorBias2D	0.171	0.000	0.171
plotControlData	0.002	0.000	0.001
plotDensity	0.102	0.000	0.102
plotGammaFit	7.566	0.004	7.578
plotHousekeepingGene	0.002	0.000	0.002
plotSampleRelation	1.010	0.020	1.032
plotStringencyGene	0.002	0.000	0.002
plotVST	0.488	0.004	0.493
probeID2nuID	3.615	0.012	3.629
produceGEOPlatformFile	0.001	0.000	0.001
produceGEOSubmissionFile	0.001	0.000	0.001
produceMethylationGEOSubmissionFile	0	0	0
seq2id	0	0	0
targetID2nuID	3.958	0.012	3.977
vst	0.435	0.004	0.439