lumi 2.23.1
Pan Du
| Snapshot Date: 2016-04-16 17:20:38 -0700 (Sat, 16 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi | | Last Changed Rev: 112482 / Revision: 116400 | | Last Changed Date: 2016-01-12 13:30:24 -0800 (Tue, 12 Jan 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ WARNINGS ] | OK | |
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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_2.23.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/lumi.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘2.23.1’
* 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 ... [24s/26s] 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-3.3-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
.estimate.quantile.reference: no visible global function definition for
‘approx’
.initialGammaEstimation: no visible global function definition for
‘quantile’
.initialGammaEstimation: no visible global function definition for
‘var’
.quantileNormalization.reference: no visible global function definition
for ‘approx’
addAnnotationInfo: no visible global function definition for ‘fData’
addAnnotationInfo: no visible global function definition for ‘start’
addAnnotationInfo: no visible global function definition for ‘keys’
addAnnotationInfo: no visible global function definition for ‘fData<-’
addNuID2lumi: no visible global function definition for ‘read.table’
addNuID2lumi: no visible global function definition for ‘notes<-’
addNuID2lumi: no visible global function definition for
‘packageDescription’
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<-’
bgAdjust: no visible binding for global variable ‘quantile’
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’
detectOutlier: no visible global function definition for ‘cor’
detectOutlier: no visible global function definition for ‘median’
detectOutlier: no visible global function definition for ‘dist’
detectOutlier: no visible global function definition for ‘hclust’
detectOutlier: no visible global function definition for ‘as.dist’
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<-’
estimateLumiCV : <anonymous>: no visible global function definition for
‘sd’
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 binding for global variable ‘median’
estimateMethylationBG: no visible global function definition for
‘assayDataElementNames’
gammaFitEM: no visible global function definition for ‘dgamma’
gammaFitEM: no visible global function definition for ‘pgamma’
getChrInfo: no visible global function definition for ‘fData’
importMethyIDAT: no visible global function definition for
‘assayDataElementNames’
importMethyIDAT: no visible global function definition for
‘assayDataElement’
lumiB: no visible global function definition for ‘packageDescription’
lumiMethyB: no visible global function definition for
‘assayDataElement’
lumiMethyB: no visible global function definition for
‘packageDescription’
lumiMethyC: no visible global function definition for
‘assayDataElement’
lumiMethyC: no visible global function definition for
‘packageDescription’
lumiMethyN: no visible global function definition for
‘assayDataElement’
lumiMethyN: no visible global function definition for
‘packageDescription’
lumiMethyStatus: no visible global function definition for
‘packageDescription’
lumiN: no visible global function definition for ‘packageDescription’
lumiQ: no visible global function definition for ‘rowMin’
lumiQ: no visible binding for global variable ‘sd’
lumiQ: no visible global function definition for ‘dist’
lumiQ: no visible global function definition for ‘packageDescription’
lumiR: no visible global function definition for ‘read.table’
lumiR: no visible global function definition for ‘write.table’
lumiR: no visible global function definition for ‘notes<-’
lumiR: no visible global function definition for ‘packageDescription’
lumiR.batch: no visible global function definition for ‘read.table’
lumiR.batch: no visible global function definition for
‘packageDescription’
lumiT: no visible global function definition for ‘packageDescription’
monoSmu: no visible global function definition for ‘supsmu’
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’
plotCDF : <anonymous>: no visible global function definition for ‘ecdf’
plotCDF: no visible global function definition for ‘Axis’
plotCDF: no visible global function definition for ‘box’
plotCDF: no visible global function definition for ‘legend’
plotColorBias1D: no visible binding for global variable
‘density.default’
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’
plotColorBias2D: no visible global function definition for ‘layout’
plotControlData: no visible global function definition for
‘assayDataElement’
plotControlData: no visible binding for global variable ‘sd’
plotControlData: no visible global function definition for ‘title’
plotControlData: no visible global function definition for ‘arrows’
plotDensity: no visible global function definition for ‘legend’
plotGammaFit: no visible global function definition for ‘dgamma’
plotHousekeepingGene: no visible global function definition for ‘title’
plotHousekeepingGene: no visible global function definition for
‘legend’
plotSampleRelation : <anonymous>: no visible global function definition
for ‘sd’
plotSampleRelation: no visible global function definition for ‘dist’
plotSampleRelation: no visible global function definition for ‘hclust’
plotSampleRelation: no visible global function definition for
‘cmdscale’
plotSampleRelation: no visible global function definition for ‘colors’
plotSampleRelation: no visible global function definition for ‘legend’
plotStringencyGene: no visible global function definition for ‘title’
plotStringencyGene: no visible global function definition for ‘legend’
plotVST: no visible global function definition for ‘legend’
produceGEOPlatformFile: no visible global function definition for
‘write.table’
produceGEOSampleInfoTemplate: no visible global function definition for
‘write.table’
produceGEOSubmissionFile: no visible global function definition for
‘read.table’
produceGEOSubmissionFile: no visible global function definition for
‘write.table’
produceMethylationGEOSubmissionFile: no visible global function
definition for ‘read.table’
produceMethylationGEOSubmissionFile: no visible global function
definition for ‘write.table’
rankinvariant: no visible global function definition for ‘tail’
rsn : pairwiseN: no visible global function definition for ‘sd’
smoothQuantileNormalization: no visible global function definition for
‘approx’
smoothQuantileNormalization: no visible global function definition for
‘sd’
ssn : <anonymous>: no visible global function definition for ‘median’
vst: no visible global function definition for ‘lm’
vst: no visible global function definition for ‘predict’
MAplot,ExpressionSet: no visible global function definition for
‘rowMin’
[,LumiBatch-ANY-ANY-ANY: no visible global function definition for
‘packageDescription’
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’
combine,LumiBatch-LumiBatch: no visible global function definition for
‘packageDescription’
density,ExpressionSet: no visible global function definition for
‘rowMin’
density,ExpressionSet: no visible global function definition for
‘legend’
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 : lowerPanel: no visible global function definition
for ‘cor’
pairs,ExpressionSet : diagPanel: no visible global function definition
for ‘rect’
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’
show,LumiBatch: no visible global function definition for ‘head’
show,LumiBatch: no visible global function definition for ‘tail’
Undefined global functions or variables:
AnnotatedDataFrame Axis approx arrows as.dist assayDataElement
assayDataElement<- assayDataElementNames assayDataElementReplace
assayDataValidMembers box cmdscale colors cor density.default
description dgamma dist ecdf fData fData<- hclust head keys layout
legend lm median notes<- packageDescription pgamma predict
protocolData protocolData<- quantile read.table rect rowMin sd start
storageMode<- supsmu tail title var write.table
Consider adding
importFrom("grDevices", "colors")
importFrom("graphics", "Axis", "arrows", "box", "layout", "legend",
"rect", "title")
importFrom("stats", "approx", "as.dist", "cmdscale", "cor",
"density.default", "dgamma", "dist", "ecdf", "hclust", "lm",
"median", "pgamma", "predict", "quantile", "sd", "start",
"supsmu", "var")
importFrom("utils", "head", "packageDescription", "read.table", "tail",
"write.table")
to your NAMESPACE file.
* 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 ... [162s/165s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 72.846 5.878 79.518
getChipInfo 5.436 0.265 6.887
methylationCall 4.718 0.330 5.087
* 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-3.3-bioc/meat/lumi.Rcheck/00check.log’
for details.