cellHTS2 2.38.0
Joseph Barry
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/cellHTS2 | | Last Changed Rev: 122710 / Revision: 128728 | | Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / 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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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings cellHTS2_2.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/cellHTS2.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.38.0’
* 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 5.7Mb
sub-directories of 1Mb or more:
KcViab 2.0Mb
doc 1.6Mb
* 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘cellHTS2’ for: ‘coerce’, ‘initialize’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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’
Bscore: no visible global function definition for ‘validObject’
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<-’
cellHTSlistVerification: no visible global function definition for ‘is’
cellHTSlistVerification: no visible binding for global variable ‘is’
chanCorrFun : <anonymous>: no visible global function definition for
‘par’
chanCorrFun : <anonymous>: no visible global function definition for
‘abline’
checkClass : <anonymous>: no visible global function definition for
‘is’
checkColumns: no visible global function definition for ‘listLen’
checkControls: no visible global function definition for ‘is’
checkMandatoryColumns: no visible global function definition for ‘slot’
checkMandatoryColumns: no visible global function definition for
‘varLabels’
checkPosControls: no visible global function definition for ‘is’
chtsImage: no visible global function definition for ‘new’
chtsImageStack: no visible binding for global variable ‘is’
chtsImageStack: no visible global function definition for ‘new’
chtsModule: no visible global function definition for ‘new’
chtsSetSetting: no visible global function definition for ‘modifyList’
colors4Controls: no visible global function definition for
‘colorRampPalette’
configurationAsScreenPlot: no visible global function definition for
‘is’
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 ‘new’
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’
convertOldCellHTS: no visible binding for global variable ‘validObject’
convertOldCellHTS: no visible global function definition for
‘validObject’
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’
gseaModule: no visible global function definition for ‘new’
gseaModule: no visible global function definition for ‘validObject’
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’
isUpToDate: no visible global function definition for ‘slotNames’
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 ‘is’
normalizePlates: no visible global function definition for ‘assayData’
normalizePlates: no visible global function definition for
‘validObject’
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 ‘is’
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 ‘new’
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 global function definition for ‘is’
readPlateList: no visible binding for global variable ‘assayDataNew’
readPlateList: no visible global function definition for ‘new’
rsa: no visible global function definition for ‘is’
rsa: no visible global function definition for ‘channelNames’
saveHtmlGlossary: no visible global function definition for ‘hwrite’
scoreReplicates: no visible global function definition for
‘validObject’
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’
spatialNormalization: no visible global function definition for ‘new’
spatialNormalization: no visible global function definition for
‘validObject’
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<-’
summarizeChannels: no visible global function definition for
‘validObject’
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’
summarizeReplicates: no visible global function definition for
‘validObject’
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’
updateCellHTS: no visible global function definition for ‘slotNames’
updateCellHTS: no visible global function definition for ‘new’
updateCellHTS: no visible global function definition for ‘slot<-’
validityCellHTS: no visible global function definition for ‘is’
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<-’
Data<-,cellHTS-array: no visible global function definition for
‘validObject’
ROC,cellHTS: no visible global function definition for ‘is’
ROC,cellHTS: no visible global function definition for ‘quantile’
ROC,cellHTS: no visible global function definition for ‘new’
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<-’
annotate,cellHTS: no visible global function definition for
‘validObject’
batch,cellHTS: no visible global function definition for ‘slot’
batch<-,cellHTS-data.frame: no visible global function definition for
‘slot’
batch<-,cellHTS-data.frame: no visible global function definition for
‘slot<-’
batch<-,cellHTS-data.frame: no visible global function definition for
‘validObject’
coerce,chtsImage-data.frame: no visible global function definition for
‘slotNames’
coerce,chtsImage-data.frame : <anonymous>: no visible global function
definition for ‘slot’
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<-’
configure,cellHTS: no visible global function definition for
‘validObject’
geneAnno,cellHTS: no visible global function definition for ‘fData’
initialize,cellHTS: no visible global function definition for
‘slotNames’
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’
initialize,cellHTS: no visible binding for global variable
‘callNextMethod’
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<-’
name<-,cellHTS-character: no visible global function definition for
‘validObject’
plate,cellHTS: no visible global function definition for ‘fData’
plateEffects,cellHTS: no visible global function definition for ‘slot’
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’
writeHtml,chtsImage: no visible global function definition for ‘as’
writeHtml,chtsModule: no visible global function definition for ‘is’
writeTab,cellHTS: no visible global function definition for
‘write.table’
Undefined global functions or variables:
IQR abline addVigs2WinMenu annotatedDataFrameFrom annotation as
assayData assayData<- assayDataElement assayDataElement<-
assayDataElementNames assayDataNew axis barplot box boxplot
brewer.pal callNextMethod 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 is layout legend listLen locfit locfit.robust mad
median medpolish modifyList mtext new 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 slot
slot<- slotNames storageMode storageMode<- tail text validObject
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("methods", "as", "callNextMethod", "is", "new", "slot",
"slot<-", "slotNames", "validObject")
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 (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Unknown package ‘cellHTS’ in Rd xrefs
* 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 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: 1 WARNING, 6 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.