cellHTS2 2.35.0
Joseph Barry
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cellHTS2 | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings cellHTS2_2.35.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/cellHTS2.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.35.0’
* 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 ... [14s/14s] OK
* checking installed package size ... NOTE
installed size is 5.7Mb
sub-directories of 1Mb or more:
KcViab 2.0Mb
doc 1.5Mb
* 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
annotate,cellHTS: warning in read.table(file.path(path, file), sep =
"\t", header = TRUE, stringsAsFactors = FALSE, na.string = "", quote
= "", fill = FALSE): partial argument match of 'na.string' to
'na.strings'
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
buildCellHTS2: no visible global function definition for ‘channelNames’
buildCellHTS2: no visible global function definition for
‘channelNames<-’
checkColumns: no visible global function definition for ‘listLen’
checkMandatoryColumns: no visible global function definition for
‘varLabels’
configurationAsScreenPlot: no visible global function definition for
‘brewer.pal’
configurationAsScreenPlot: no visible global function definition for
‘plotScreen’
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’
envisionPlateReader: no visible global function definition for
‘listLen’
getConfiguration: no visible global function definition for ‘listLen’
getTopTable: no visible global function definition for ‘fData’
imageScreen: no visible global function definition for ‘brewer.pal’
imageScreen: no visible global function definition for ‘fData’
isUpToDate: no visible global function definition for ‘getObjectSlots’
normalizePlates: no visible global function definition for ‘assayData’
perCatPage: no visible global function definition for ‘hwrite’
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’
scores2calls: no visible global function definition for ‘assayData<-’
scores2calls: no visible global function definition for ‘assayDataNew’
scores2calls: no visible global function definition for ‘featureNames’
spatialNormalization: no visible global function definition for
‘locfit’
spatialNormalization: no visible binding for global variable
‘locfit.robust’
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 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’
updateCellHTS: no visible global function definition for
‘getObjectSlots’
validityCellHTS: no visible global function definition for ‘assayData’
validityCellHTS: no visible global function definition for
‘assayDataElementNames’
writeHtml.gseaModule: no visible global function definition for
‘hwrite’
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’
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<-’
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’
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’
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’
Undefined global functions or variables:
addVigs2WinMenu annotatedDataFrameFrom annotation assayData
assayData<- assayDataElement assayDataElement<- assayDataElementNames
assayDataNew brewer.pal channel channelNames channelNames<-
description<- experimentData fData fData<- featureData featureNames
featureNames<- fvarMetadata fvarMetadata<- getObjectSlots hwrite
hwriteImage listLen locfit locfit.robust notes<- pData pData<-
package.version phenoData phenoData<- plotScreen pubMedIds rowMedians
sampleNames sampleNames<- storageMode storageMode<- varLabels
varMetadata varMetadata<-
* 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 ... [37s/37s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test.R’ [31s/31s]
[31s/31s] 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
‘/home/biocbuild/bbs-3.3-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.