BioC 3.2: CHECK report for lumi on perceval

Package: lumi

Version: 2.21.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.21.2.tar.gz

StartedAt: 2015-08-24 02:14:44 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:25:20 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 635.7 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_2.21.2.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 (2015-08-14 r69078)
* 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 ‘2.21.2’
* 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 ... [35s/46s] 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
Packages unavailable to check Rd xrefs: ‘bigmemoryExtras’, ‘hdrcde’
* 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 ... [257s/258s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
lumiMethyStatus 111.018 17.365 128.685
plotGammaFit      7.834  1.325   9.220
getChipInfo       8.299  0.550   9.112
nuID2IlluminaID   8.116  0.277   8.424
methylationCall   7.313  0.922   8.272
probeID2nuID      7.295  0.301   7.847
nuID2targetID     7.201  0.256   7.493
nuID2probeID      6.950  0.239   7.206
MAplot-methods    6.831  0.059   6.967
gammaFitEM        6.334  0.025   6.409
targetID2nuID     5.349  0.256   5.612
* 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	2.447	0.090	2.537
MAplot-methods	6.831	0.059	6.967
addAnnotationInfo	0.080	0.006	0.088
addControlData2lumi	0.000	0.000	0.001
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	2.988	0.038	3.060
adjColorBias.ssn	0.690	0.013	0.704
bgAdjust	0.087	0.007	0.093
bgAdjustMethylation	1.059	0.011	1.070
boxplot-MethyLumiM-methods	0.739	0.021	0.761
boxplot-methods	0.136	0.008	0.144
boxplotColorBias	1.106	0.031	1.137
density-methods	0.102	0.012	0.114
detectOutlier	0.122	0.014	0.136
detectionCall	0.178	0.017	0.195
estimateBeta	0.927	0.014	0.940
estimateIntensity	0.167	0.015	0.183
estimateLumiCV	0.120	0.021	0.142
estimateM	0.696	0.027	0.723
estimateMethylationBG	0.256	0.005	0.261
example.lumi	0.088	0.009	0.097
example.lumiMethy	0.858	0.007	0.865
example.methyTitration	0.186	0.012	0.197
gammaFitEM	6.334	0.025	6.409
getChipInfo	8.299	0.550	9.112
getControlData	0.003	0.001	0.003
getControlProbe	0.002	0.000	0.002
getControlType	0.002	0.001	0.002
getNuIDMappingInfo	2.186	0.111	2.309
hist-methods	0.134	0.012	0.148
id2seq	0.002	0.000	0.002
inverseVST	1.943	0.029	1.983
is.nuID	0.001	0.001	0.002
lumiB	0.092	0.014	0.107
lumiExpresso	0.311	0.040	0.352
lumiMethyB	0.062	0.006	0.068
lumiMethyC	2.012	0.155	2.183
lumiMethyN	0.126	0.014	0.140
lumiMethyStatus	111.018	17.365	128.685
lumiN	0.633	0.033	0.674
lumiQ	0.297	0.028	0.330
lumiR	0.001	0.000	0.001
lumiR.batch	0.001	0.000	0.001
lumiT	0.471	0.037	0.529
methylationCall	7.313	0.922	8.272
normalizeMethylation.quantile	0.231	0.021	0.252
normalizeMethylation.ssn	0.285	0.017	0.300
nuID2EntrezID	1.801	0.066	1.867
nuID2IlluminaID	8.116	0.277	8.424
nuID2RefSeqID	3.177	0.074	3.258
nuID2probeID	6.950	0.239	7.206
nuID2targetID	7.201	0.256	7.493
pairs-methods	2.486	0.117	2.606
plot-methods	2.845	0.094	3.096
plotCDF	0.162	0.028	0.191
plotColorBias1D	0.327	0.028	0.358
plotColorBias2D	0.410	0.021	0.434
plotControlData	0.003	0.001	0.002
plotDensity	0.143	0.014	0.158
plotGammaFit	7.834	1.325	9.220
plotHousekeepingGene	0.002	0.000	0.003
plotSampleRelation	0.976	0.045	1.024
plotStringencyGene	0.002	0.000	0.002
plotVST	0.459	0.032	0.498
probeID2nuID	7.295	0.301	7.847
produceGEOPlatformFile	0.000	0.000	0.001
produceGEOSubmissionFile	0	0	0
produceMethylationGEOSubmissionFile	0.000	0.000	0.001
seq2id	0.002	0.000	0.001
targetID2nuID	5.349	0.256	5.612
vst	0.512	0.024	0.542