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BioC 3.4: CHECK report for lumi on moscato1

This page was generated on 2016-08-19 02:41:26 -0700 (Fri, 19 Aug 2016).

Package 664/1245HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.25.0
Pan Du
Snapshot Date: 2016-08-17 19:15:45 -0700 (Wed, 17 Aug 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/lumi
Last Changed Rev: 117081 / Revision: 120233
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: lumi
Version: 2.25.0
Command: rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.25.0.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.25.0.tar.gz
StartedAt: 2016-08-18 12:10:23 -0700 (Thu, 18 Aug 2016)
EndedAt: 2016-08-18 12:22:04 -0700 (Thu, 18 Aug 2016)
EllapsedTime: 701.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.25.0.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/lumi.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lumi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'lumi' version '2.25.0'
* 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 whether package 'lumi' can be installed ... 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 'D:/biocbld/bbs-3.4-bioc/meat/lumi.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 79.06   0.00   79.08
MAplot-methods   5.48   0.02    5.49
getChipInfo      4.55   0.08   19.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
lumiMethyStatus 86.30   0.00   86.31
MAplot-methods   6.01   0.02    6.06
* 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
  'D:/biocbld/bbs-3.4-bioc/meat/lumi.Rcheck/00check.log'
for details.


lumi.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'lumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lumi' as lumi_2.25.0.zip
* DONE (lumi)

lumi.Rcheck/examples_i386/lumi-Ex.timings:

nameusersystemelapsed
LumiBatch-class1.740.001.73
MAplot-methods5.480.025.49
addAnnotationInfo0.060.000.06
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile1.810.001.81
adjColorBias.ssn0.890.011.03
bgAdjust0.090.020.11
bgAdjustMethylation0.240.000.23
boxplot-MethyLumiM-methods1.090.001.94
boxplot-methods0.480.000.48
boxplotColorBias0.190.010.20
density-methods0.120.000.13
detectOutlier0.100.020.11
detectionCall0.20.00.2
estimateBeta0.120.000.13
estimateIntensity0.160.020.17
estimateLumiCV0.140.000.14
estimateM0.890.000.89
estimateMethylationBG0.190.000.18
example.lumi0.080.010.10
example.lumiMethy0.060.000.07
example.methyTitration0.220.000.22
gammaFitEM4.510.004.51
getChipInfo 4.55 0.0819.39
getControlData000
getControlProbe000
getControlType000
getNuIDMappingInfo1.140.023.07
hist-methods0.230.000.23
id2seq000
inverseVST0.560.010.73
is.nuID000
lumiB0.090.000.10
lumiExpresso0.370.000.38
lumiMethyB0.110.000.10
lumiMethyC1.900.022.03
lumiMethyN0.110.010.12
lumiMethyStatus79.06 0.0079.08
lumiN0.580.000.64
lumiQ0.350.000.36
lumiR000
lumiR.batch000
lumiT0.520.000.51
methylationCall4.880.004.89
normalizeMethylation.quantile0.190.020.20
normalizeMethylation.ssn0.20.00.2
nuID2EntrezID1.130.011.14
nuID2IlluminaID3.860.003.87
nuID2RefSeqID1.120.021.14
nuID2probeID3.290.003.29
nuID2targetID3.460.013.47
pairs-methods1.580.021.60
plot-methods2.350.002.35
plotCDF0.190.000.19
plotColorBias1D0.310.000.31
plotColorBias2D0.220.000.22
plotControlData000
plotDensity0.140.020.16
plotGammaFit4.430.014.44
plotHousekeepingGene000
plotSampleRelation0.780.000.78
plotStringencyGene000
plotVST0.480.000.48
probeID2nuID3.360.003.36
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID3.080.023.09
vst0.310.000.32

lumi.Rcheck/examples_x64/lumi-Ex.timings:

nameusersystemelapsed
LumiBatch-class1.860.071.94
MAplot-methods6.010.026.06
addAnnotationInfo0.070.000.08
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile1.470.001.95
adjColorBias.ssn0.830.020.84
bgAdjust0.120.000.13
bgAdjustMethylation0.250.010.26
boxplot-MethyLumiM-methods1.30.01.3
boxplot-methods0.090.000.09
boxplotColorBias0.190.000.19
density-methods0.090.020.11
detectOutlier0.100.000.09
detectionCall0.140.010.16
estimateBeta0.100.020.12
estimateIntensity0.600.010.91
estimateLumiCV0.120.000.12
estimateM0.840.020.86
estimateMethylationBG0.180.000.17
example.lumi0.090.000.10
example.lumiMethy0.060.020.08
example.methyTitration0.190.010.20
gammaFitEM4.790.024.87
getChipInfo4.510.124.63
getControlData000
getControlProbe000
getControlType000
getNuIDMappingInfo1.810.061.87
hist-methods0.130.000.13
id2seq000
inverseVST0.530.020.57
is.nuID000
lumiB0.120.000.13
lumiExpresso0.300.010.31
lumiMethyB0.090.000.09
lumiMethyC1.780.021.80
lumiMethyN0.090.020.11
lumiMethyStatus86.30 0.0086.31
lumiN0.610.001.48
lumiQ0.810.000.82
lumiR0.020.000.01
lumiR.batch000
lumiT0.470.000.47
methylationCall4.930.004.93
normalizeMethylation.quantile0.650.000.65
normalizeMethylation.ssn0.190.010.21
nuID2EntrezID1.780.001.77
nuID2IlluminaID3.700.083.78
nuID2RefSeqID1.340.021.36
nuID2probeID4.320.014.33
nuID2targetID3.660.023.69
pairs-methods1.220.001.96
plot-methods2.470.032.50
plotCDF0.210.000.22
plotColorBias1D0.320.010.51
plotColorBias2D0.20.00.2
plotControlData000
plotDensity0.190.000.19
plotGammaFit4.930.004.93
plotHousekeepingGene000
plotSampleRelation1.030.021.04
plotStringencyGene000
plotVST0.420.000.43
probeID2nuID3.230.013.24
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID3.850.003.85
vst0.270.000.26