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BioC 3.3: CHECK report for cellHTS2 on moscato2

This page was generated on 2016-10-13 12:48:19 -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: rm -rf cellHTS2.buildbin-libdir cellHTS2.Rcheck && mkdir cellHTS2.buildbin-libdir cellHTS2.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.36.0.tar.gz >cellHTS2.Rcheck\00install.out 2>&1 && cp cellHTS2.Rcheck\00install.out cellHTS2-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.36.0.tar.gz
StartedAt: 2016-10-13 01:49:20 -0700 (Thu, 13 Oct 2016)
EndedAt: 2016-10-13 01:59:48 -0700 (Thu, 13 Oct 2016)
EllapsedTime: 627.1 seconds
RetCode: 0
Status:  OK  
CheckDir: cellHTS2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf cellHTS2.buildbin-libdir cellHTS2.Rcheck && mkdir cellHTS2.buildbin-libdir cellHTS2.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.36.0.tar.gz >cellHTS2.Rcheck\00install.out 2>&1 && cp cellHTS2.Rcheck\00install.out cellHTS2-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/cellHTS2.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 '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 whether package 'cellHTS2' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  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
* 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R'
 OK
** running tests for arch 'x64' ...
  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
  'E:/biocbld/bbs-3.3-bioc/meat/cellHTS2.Rcheck/00check.log'
for details.


cellHTS2.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'cellHTS2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellHTS2' as cellHTS2_2.36.0.zip
* DONE (cellHTS2)

cellHTS2.Rcheck/examples_i386/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore3.400.013.42
ROC-class0.270.000.27
ROC1.380.001.39
annotate1.200.001.21
bdgpbiomart0.300.010.31
buildCellHTS20.460.000.47
cellHTS-class2.140.052.20
configurationAsScreenPlot2.930.003.28
configure1.170.001.17
convertOldCellHTS101
convertWellCoordinates000
data-KcViab0.210.000.20
data-KcViabSmall0.010.000.01
data-dualCh0.020.000.02
data-oldKcViabSmall0.030.000.03
getDynamicRange0.890.000.89
getEnVisionRawData0.040.000.05
getMeasureRepAgreement0.50.00.5
getTopTable1.660.001.65
getZfactor0.780.000.78
imageScreen1.280.011.29
normalizePlates1.450.021.47
oneRowPerId000
plotSpatialEffects2.070.002.08
readHTAnalystData1.170.021.18
readPlateList0.610.010.72
rsa1.110.021.12
scoreReplicates0.930.000.94
scores2calls1.020.001.29
setSettings0.010.000.02
spatialNormalization1.280.001.28
summarizeChannels2.340.002.35
summarizeReplicates0.910.000.91
templateDescriptionFile000
updateCellHTS0.120.000.12
write.tabdel0.060.000.07
writeReport0.020.000.01
writeTab0.020.010.03

cellHTS2.Rcheck/examples_x64/cellHTS2-Ex.timings:

nameusersystemelapsed
Bscore3.540.053.59
ROC-class0.280.010.29
ROC1.480.001.49
annotate1.360.001.35
bdgpbiomart0.200.000.21
buildCellHTS20.360.000.35
cellHTS-class2.290.032.33
configurationAsScreenPlot2.080.002.07
configure0.780.000.78
convertOldCellHTS0.810.000.81
convertWellCoordinates000
data-KcViab0.140.020.16
data-KcViabSmall0.020.000.01
data-dualCh0.020.000.01
data-oldKcViabSmall0.020.000.02
getDynamicRange0.70.00.7
getEnVisionRawData0.030.000.03
getMeasureRepAgreement0.580.000.58
getTopTable1.530.001.68
getZfactor0.450.020.47
imageScreen1.300.011.31
normalizePlates1.590.001.59
oneRowPerId000
plotSpatialEffects2.570.002.57
readHTAnalystData1.520.001.52
readPlateList1.010.001.37
rsa1.830.001.82
scoreReplicates1.180.021.21
scores2calls1.340.001.40
setSettings0.020.000.02
spatialNormalization1.320.011.34
summarizeChannels2.920.002.91
summarizeReplicates1.470.001.47
templateDescriptionFile000
updateCellHTS0.140.020.16
write.tabdel0.050.010.06
writeReport0.000.020.02
writeTab0.010.020.03