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BioC 3.3: CHECK report for cellHTS2 on oaxaca

This page was generated on 2016-10-13 12:56:21 -0700 (Thu, 13 Oct 2016).

Package 157/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS2 2.36.0
Joseph Barry
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/cellHTS2
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: cellHTS2
Version: 2.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellHTS2_2.36.0.tar.gz
StartedAt: 2016-10-12 23:55:45 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-13 00:00:44 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 299.0 seconds
RetCode: 0
Status:  OK 
CheckDir: cellHTS2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellHTS2_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/cellHTS2.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.36.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘RColorBrewer’ ‘Biobase’ ‘genefilter’ ‘splots’ ‘vsn’ ‘hwriter’
  ‘locfit’ ‘grid’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘cellHTS2’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      1.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘genefilter’ ‘hwriter’ ‘locfit’ ‘splots’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘Biobase:::.showAnnotatedDataFrame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
Bscore: no visible global function definition for ‘medpolish’
OPIScore : <anonymous>: no visible global function definition for
  ‘phyper’
QMexperiment : <anonymous>: no visible global function definition for
  ‘par’
adjustVariancebyBatch: no visible global function definition for ‘mad’
adjustVariancebyExperiment : <anonymous>: no visible global function
  definition for ‘mad’
adjustVariancebyPlate : <anonymous>: no visible global function
  definition for ‘mad’
barplotWithImageMap: no visible global function definition for
  ‘barplot’
barplotWithImageMap: no visible global function definition for ‘par’
barplotWithImageMap: no visible global function definition for
  ‘dev.size’
boxplotwithNA: no visible global function definition for ‘boxplot’
boxplotwithNA: no visible global function definition for ‘IQR’
boxplotwithNA: no visible global function definition for ‘axis’
boxplotwithNA: no visible global function definition for ‘abline’
boxplotwithNA: no visible global function definition for ‘box’
buildCellHTS2: no visible global function definition for ‘channelNames’
buildCellHTS2: no visible global function definition for
  ‘channelNames<-’
chanCorrFun : <anonymous>: no visible global function definition for
  ‘par’
chanCorrFun : <anonymous>: no visible global function definition for
  ‘abline’
checkColumns: no visible global function definition for ‘listLen’
checkMandatoryColumns: no visible global function definition for
  ‘varLabels’
chtsSetSetting: no visible global function definition for ‘modifyList’
colors4Controls: no visible global function definition for
  ‘colorRampPalette’
configurationAsScreenPlot: no visible global function definition for
  ‘brewer.pal’
configurationAsScreenPlot: no visible global function definition for
  ‘colorRampPalette’
configurationAsScreenPlot: no visible global function definition for
  ‘rainbow’
configurationAsScreenPlot: no visible global function definition for
  ‘plotScreen’
controlsplot: no visible global function definition for ‘legend’
controlsplot: no visible global function definition for ‘segments’
controlsplot: no visible global function definition for ‘points’
controlsplot: no visible global function definition for ‘axis’
controlsplot: no visible global function definition for ‘abline’
convertOldCellHTS: no visible global function definition for
  ‘assayDataNew’
convertOldCellHTS: no visible global function definition for
  ‘storageMode<-’
convertOldCellHTS: no visible global function definition for ‘pData<-’
convertOldCellHTS: no visible global function definition for
  ‘varMetadata’
convertOldCellHTS: no visible global function definition for
  ‘varMetadata<-’
convertOldCellHTS: no visible global function definition for ‘notes<-’
convertOldCellHTS: no visible global function definition for
  ‘description<-’
convertOldCellHTS: no visible global function definition for ‘fData’
convertOldCellHTS: no visible global function definition for ‘fData<-’
convertOldCellHTS: no visible global function definition for
  ‘fvarMetadata’
convertOldCellHTS: no visible global function definition for
  ‘fvarMetadata<-’
convertOldCellHTS: no visible global function definition for
  ‘assayData<-’
convertOldCellHTS: no visible global function definition for
  ‘featureNames’
corrFun : <anonymous>: no visible global function definition for ‘par’
corrFun : <anonymous>: no visible global function definition for
  ‘abline’
corrFun: no visible global function definition for ‘cor’
corrFun: no visible global function definition for ‘colorRampPalette’
corrFun : <anonymous>: no visible global function definition for
  ‘layout’
corrFun : <anonymous>: no visible global function definition for
  ‘image’
corrFun : <anonymous>: no visible global function definition for ‘box’
corrFun : <anonymous>: no visible global function definition for ‘axis’
densityplot: no visible global function definition for ‘density’
densityplot: no visible global function definition for ‘legend’
envisionPlateReader: no visible global function definition for
  ‘listLen’
envisionPlateReader: no visible global function definition for
  ‘write.table’
getConfiguration: no visible global function definition for ‘listLen’
getConfiguration: no visible global function definition for
  ‘read.table’
getMeasureRepAgreement: no visible binding for global variable ‘sd’
getMeasureRepAgreement: no visible global function definition for
  ‘combn’
getMeasureRepAgreement: no visible global function definition for ‘cor’
getPlist: no visible global function definition for ‘read.table’
getScreenlog: no visible global function definition for ‘read.table’
getTopTable: no visible binding for global variable ‘median’
getTopTable : <anonymous>: no visible global function definition for
  ‘median’
getTopTable: no visible global function definition for ‘fData’
getZfactor: no visible binding for global variable ‘median’
getZfactor: no visible binding for global variable ‘mad’
getZfactor: no visible binding for global variable ‘sd’
guid: no visible global function definition for ‘runif’
histFun : histfun: no visible global function definition for ‘par’
histFun : histfun: no visible global function definition for ‘hist’
histFun : histfun: no visible global function definition for ‘gray’
histFun : histfun: no visible global function definition for ‘rug’
histFun : densfun: no visible global function definition for ‘par’
histFun : densfun: no visible global function definition for ‘density’
histFun : densfun: no visible global function definition for ‘axis’
histFun : densfun: no visible global function definition for ‘abline’
histFun : densfun: no visible global function definition for ‘points’
imageScreen: no visible global function definition for ‘brewer.pal’
imageScreen: no visible global function definition for ‘fData’
imageScreen: no visible global function definition for
  ‘colorRampPalette’
imageScreen: no visible global function definition for ‘par’
imageScreen: no visible global function definition for ‘image’
imageScreen: no visible global function definition for ‘text’
isUpToDate: no visible global function definition for ‘getObjectSlots’
maFun : <anonymous>: no visible global function definition for ‘par’
maFun : <anonymous>: no visible global function definition for ‘abline’
makePlot: no visible global function definition for ‘pdf’
makePlot: no visible global function definition for ‘dev.off’
makePlot: no visible global function definition for ‘png’
normalizePlates: no visible global function definition for ‘assayData’
parseGlossaryXML: no visible global function definition for ‘tail’
perCatPage: no visible global function definition for ‘hwrite’
perPlateScaling: no visible binding for global variable ‘median’
plotSpatialEffects: no visible global function definition for
  ‘brewer.pal’
readHTAnalystData: no visible global function definition for ‘listLen’
readHTAnalystData: no visible global function definition for
  ‘assayDataNew’
readHTAnalystData: no visible global function definition for
  ‘storageMode<-’
readHTAnalystData: no visible global function definition for ‘pData<-’
readHTAnalystData: no visible global function definition for
  ‘varMetadata’
readHTAnalystData: no visible global function definition for
  ‘varMetadata<-’
readHTAnalystOneReplicate: no visible global function definition for
  ‘listLen’
readPlateList: no visible binding for global variable ‘assayDataNew’
rsa: no visible global function definition for ‘channelNames’
saveHtmlGlossary: no visible global function definition for ‘hwrite’
scoreReplicatesByNPI: no visible binding for global variable ‘channel’
scoreReplicatesByzscore : <anonymous>: no visible global function
  definition for ‘median’
scoreReplicatesByzscore : <anonymous>: no visible global function
  definition for ‘mad’
scores2calls: no visible global function definition for ‘assayData<-’
scores2calls: no visible global function definition for ‘assayDataNew’
scores2calls: no visible global function definition for ‘featureNames’
sdFun : statWithNA: no visible binding for global variable ‘sd’
spatialNormalization: no visible global function definition for
  ‘locfit’
spatialNormalization: no visible binding for global variable
  ‘locfit.robust’
spatialNormalization: no visible global function definition for
  ‘predict’
summarizeChannels: no visible global function definition for
  ‘channelNames’
summarizeChannels: no visible global function definition for
  ‘assayDataElementNames’
summarizeChannels: no visible global function definition for
  ‘assayDataElement<-’
summarizeChannels: no visible global function definition for
  ‘channelNames<-’
summarizeReplicates: no visible global function definition for
  ‘rowMedians’
summarizeReplicates: no visible binding for global variable ‘median’
summarizeReplicates: no visible global function definition for
  ‘featureNames’
summarizeReplicates: no visible global function definition for
  ‘channelNames’
summarizeReplicates : <anonymous>: no visible global function
  definition for ‘featureNames’
summarizeReplicates: no visible global function definition for
  ‘assayData<-’
summarizeReplicates: no visible binding for global variable
  ‘assayDataNew’
tableOutput: no visible global function definition for ‘read.table’
tableOutputWithHeaderRows: no visible global function definition for
  ‘read.table’
updateCellHTS: no visible global function definition for
  ‘getObjectSlots’
validityCellHTS: no visible global function definition for ‘assayData’
validityCellHTS: no visible global function definition for
  ‘assayDataElementNames’
write.tabdel: no visible global function definition for ‘write.table’
writeHtml.gseaModule: no visible global function definition for
  ‘hwrite’
writeHtml.gseaModule: no visible global function definition for
  ‘write.table’
writeHtml.mainpage: no visible global function definition for
  ‘package.version’
writeHtml.plateConf: no visible global function definition for ‘hwrite’
writeHtml.plateList: no visible global function definition for
  ‘channelNames’
writeHtml.screenResults: no visible global function definition for
  ‘hwrite’
writeHtml.screenSummary : <anonymous>: no visible global function
  definition for ‘par’
writeHtml.screenSummary : <anonymous>: no visible global function
  definition for ‘qqnorm’
writeHtml.screenSummary : <anonymous>: no visible global function
  definition for ‘qqline’
writeHtml.screenSummary : <anonymous>: no visible global function
  definition for ‘density’
writeHtml.screenSummary : <anonymous>: no visible global function
  definition for ‘points’
writeImgRef: no visible global function definition for ‘hwrite’
writeImgRef: no visible global function definition for ‘hwriteImage’
writeQCTable: no visible global function definition for ‘hwrite’
writeReport: no visible global function definition for ‘fData’
Data,cellHTS: no visible global function definition for ‘channelNames’
Data,cellHTS: no visible global function definition for ‘featureNames’
Data,cellHTS: no visible global function definition for ‘sampleNames’
Data,cellHTS : <anonymous>: no visible global function definition for
  ‘assayDataElement’
Data<-,cellHTS-array: no visible global function definition for
  ‘channelNames’
Data<-,cellHTS-array: no visible global function definition for
  ‘featureNames’
Data<-,cellHTS-array: no visible global function definition for
  ‘sampleNames’
Data<-,cellHTS-array: no visible global function definition for
  ‘assayDataElement<-’
Data<-,cellHTS-array: no visible global function definition for
  ‘phenoData’
Data<-,cellHTS-array: no visible global function definition for
  ‘sampleNames<-’
Data<-,cellHTS-array: no visible global function definition for
  ‘phenoData<-’
Data<-,cellHTS-array: no visible global function definition for
  ‘featureNames<-’
ROC,cellHTS: no visible global function definition for ‘quantile’
annotate,cellHTS: no visible global function definition for
  ‘read.table’
annotate,cellHTS: no visible global function definition for ‘fData’
annotate,cellHTS: no visible global function definition for ‘fData<-’
annotate,cellHTS: no visible global function definition for
  ‘fvarMetadata’
annotate,cellHTS: no visible global function definition for
  ‘fvarMetadata<-’
compare2cellHTS,cellHTS-cellHTS: no visible global function definition
  for ‘experimentData’
configure,cellHTS: no visible global function definition for
  ‘channelNames’
configure,cellHTS: no visible global function definition for ‘notes<-’
configure,cellHTS: no visible global function definition for ‘fData’
configure,cellHTS: no visible global function definition for ‘fData<-’
configure,cellHTS: no visible global function definition for
  ‘description<-’
geneAnno,cellHTS: no visible global function definition for ‘fData’
initialize,cellHTS: no visible binding for global variable
  ‘assayDataNew’
initialize,cellHTS: no visible global function definition for
  ‘annotatedDataFrameFrom’
initialize,cellHTS: no visible global function definition for ‘pData<-’
initialize,cellHTS: no visible global function definition for
  ‘varMetadata<-’
initialize,cellHTS: no visible global function definition for
  ‘varMetadata’
initialize,cellHTS: no visible global function definition for
  ‘assayDataElementNames’
initialize,cellHTS: no visible global function definition for
  ‘storageMode’
initialize,cellHTS : <anonymous>: no visible global function definition
  for ‘sampleNames’
initialize,cellHTS: no visible global function definition for
  ‘sampleNames<-’
initialize,cellHTS: no visible global function definition for
  ‘sampleNames’
meanSdPlot,cellHTS: no visible global function definition for ‘par’
name,cellHTS: no visible global function definition for ‘pData’
name<-,cellHTS-character: no visible global function definition for
  ‘pData’
name<-,cellHTS-character: no visible global function definition for
  ‘pData<-’
plate,cellHTS: no visible global function definition for ‘fData’
plot,ROC-missing: no visible global function definition for ‘mtext’
show,cellHTS: no visible global function definition for ‘storageMode’
show,cellHTS: no visible global function definition for
  ‘assayDataElementNames’
show,cellHTS: no visible global function definition for ‘phenoData’
show,cellHTS: no visible global function definition for ‘featureData’
show,cellHTS: no visible global function definition for ‘pubMedIds’
show,cellHTS: no visible global function definition for ‘annotation’
well,cellHTS: no visible global function definition for ‘fData’
wellAnno,cellHTS: no visible global function definition for ‘fData’
writeTab,cellHTS: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  IQR abline addVigs2WinMenu annotatedDataFrameFrom annotation
  assayData assayData<- assayDataElement assayDataElement<-
  assayDataElementNames assayDataNew axis barplot box boxplot
  brewer.pal channel channelNames channelNames<- colorRampPalette combn
  cor density description<- dev.off dev.size experimentData fData
  fData<- featureData featureNames featureNames<- fvarMetadata
  fvarMetadata<- getObjectSlots gray hist hwrite hwriteImage image
  layout legend listLen locfit locfit.robust mad median medpolish
  modifyList mtext notes<- pData pData<- package.version par pdf
  phenoData phenoData<- phyper plotScreen png points predict pubMedIds
  qqline qqnorm quantile rainbow read.table rowMedians rug runif
  sampleNames sampleNames<- sd segments storageMode storageMode<- tail
  text varLabels varMetadata varMetadata<- write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "dev.size",
             "gray", "pdf", "png", "rainbow")
  importFrom("graphics", "abline", "axis", "barplot", "box", "boxplot",
             "hist", "image", "layout", "legend", "mtext", "par",
             "points", "rug", "segments", "text")
  importFrom("stats", "IQR", "cor", "density", "mad", "median",
             "medpolish", "phyper", "predict", "qqline", "qqnorm",
             "quantile", "runif", "sd")
  importFrom("utils", "combn", "modifyList", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  ‘GO.db’ ‘KEGG.db’
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.

cellHTS2.Rcheck/00install.out:

* installing *source* package ‘cellHTS2’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘cellHTS2’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cellHTS2)

cellHTS2.Rcheck/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore3.6020.0413.648
ROC-class0.3680.0113.798
ROC1.0120.0131.732
annotate0.7400.0030.742
bdgpbiomart0.2440.0140.259
buildCellHTS20.4150.0020.417
cellHTS-class1.9790.0514.517
configurationAsScreenPlot2.2550.0292.290
configure0.9110.0030.916
convertOldCellHTS0.9450.0090.956
convertWellCoordinates0.0010.0000.001
data-KcViab0.1730.0100.183
data-KcViabSmall0.0140.0080.022
data-dualCh0.0150.0080.024
data-oldKcViabSmall0.0140.0090.022
getDynamicRange0.8240.0100.837
getEnVisionRawData0.0760.0020.077
getMeasureRepAgreement0.6620.0110.674
getTopTable1.6440.0121.658
getZfactor0.4570.0090.467
imageScreen1.3290.0091.343
normalizePlates1.8380.0231.863
oneRowPerId0.0020.0000.003
plotSpatialEffects2.4800.0132.497
readHTAnalystData1.1450.0021.150
readPlateList0.8880.0060.895
rsa1.2120.0091.224
scoreReplicates1.5020.0121.521
scores2calls1.3800.0121.394
setSettings0.0070.0030.010
spatialNormalization1.4190.0131.434
summarizeChannels2.5330.0112.549
summarizeReplicates1.2250.0091.236
templateDescriptionFile0.0030.0010.003
updateCellHTS0.1330.0080.142
write.tabdel0.0690.0080.079
writeReport0.0100.0070.018
writeTab0.0220.0080.031