BioC 3.1: CHECK report for lumi on morelia

Package: lumi

Version: 2.20.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings lumi_2.20.2.tar.gz

StartedAt: 2015-10-09 03:24:58 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:31:46 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 407.8 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_2.20.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘2.20.2’
* 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 ... [22s/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-3.1-bioc/meat/lumi.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.2Mb
* 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
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 ... [153s/154s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
lumiMethyStatus 66.038  8.272  74.452
getChipInfo      4.240  0.463   5.943
* 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-3.1-bioc/meat/lumi.Rcheck/00check.log’
for details.

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** 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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (lumi)

name	user	system	elapsed
LumiBatch-class	1.839	0.030	1.870
MAplot-methods	3.902	0.225	4.135
addAnnotationInfo	0.054	0.011	0.065
addControlData2lumi	0.000	0.001	0.000
addNuID2lumi	0.001	0.000	0.001
adjColorBias.quantile	1.498	0.074	1.589
adjColorBias.ssn	0.517	0.054	0.578
bgAdjust	0.063	0.003	0.066
bgAdjustMethylation	0.474	0.004	0.479
boxplot-MethyLumiM-methods	0.538	0.043	0.582
boxplot-methods	0.418	0.010	0.429
boxplotColorBias	0.217	0.012	0.229
density-methods	0.085	0.028	0.114
detectOutlier	0.093	0.008	0.102
detectionCall	0.135	0.008	0.142
estimateBeta	0.081	0.004	0.086
estimateIntensity	0.172	0.007	0.180
estimateLumiCV	0.125	0.027	0.166
estimateM	0.578	0.057	0.636
estimateMethylationBG	0.187	0.001	0.188
example.lumi	0.095	0.004	0.099
example.lumiMethy	0.064	0.003	0.068
example.methyTitration	0.467	0.006	0.474
gammaFitEM	3.236	0.191	3.462
getChipInfo	4.240	0.463	5.943
getControlData	0.002	0.000	0.002
getControlProbe	0.001	0.000	0.002
getControlType	0.001	0.001	0.001
getNuIDMappingInfo	1.438	0.103	1.560
hist-methods	0.146	0.015	0.161
id2seq	0.001	0.000	0.001
inverseVST	0.488	0.034	0.522
is.nuID	0.001	0.000	0.001
lumiB	0.081	0.014	0.095
lumiExpresso	0.242	0.021	0.263
lumiMethyB	0.049	0.004	0.053
lumiMethyC	1.484	0.021	1.508
lumiMethyN	0.072	0.002	0.072
lumiMethyStatus	66.038	8.272	74.452
lumiN	0.540	0.039	0.610
lumiQ	0.277	0.040	0.321
lumiR	0.001	0.000	0.001
lumiR.batch	0.000	0.000	0.001
lumiT	0.364	0.073	0.444
methylationCall	4.517	0.419	4.942
normalizeMethylation.quantile	0.182	0.046	0.228
normalizeMethylation.ssn	0.227	0.028	0.255
nuID2EntrezID	1.373	0.085	1.458
nuID2IlluminaID	4.521	0.182	4.709
nuID2RefSeqID	1.205	0.047	1.253
nuID2probeID	4.197	0.293	4.493
nuID2targetID	4.162	0.251	4.417
pairs-methods	1.354	0.055	1.414
plot-methods	1.852	0.066	1.941
plotCDF	0.129	0.021	0.151
plotColorBias1D	0.273	0.038	0.314
plotColorBias2D	0.274	0.003	0.279
plotControlData	0.001	0.000	0.001
plotDensity	0.127	0.005	0.134
plotGammaFit	3.877	0.531	4.412
plotHousekeepingGene	0.002	0.000	0.002
plotSampleRelation	0.935	0.055	0.995
plotStringencyGene	0.001	0.000	0.001
plotVST	0.380	0.021	0.406
probeID2nuID	3.951	0.221	4.175
produceGEOPlatformFile	0.001	0.000	0.001
produceGEOSubmissionFile	0.001	0.000	0.001
produceMethylationGEOSubmissionFile	0.001	0.001	0.001
seq2id	0.001	0.000	0.001
targetID2nuID	3.943	0.237	4.187
vst	0.873	0.051	0.926