BioC 3.1: CHECK report for cellHTS2 on petty

Package: cellHTS2

Version: 2.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellHTS2_2.32.0.tar.gz

StartedAt: 2015-10-08 21:55:55 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:02:42 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 406.8 seconds

RetCode: 0

Status:  OK

CheckDir: cellHTS2.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cellHTS2_2.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/cellHTS2.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cellHTS2/DESCRIPTION’ ... OK
* this is package ‘cellHTS2’ version ‘2.32.0’
* 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 ... [26s/27s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc      1.7Mb
    KcViab   2.0Mb
* 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:
  ‘genefilter’ ‘hwriter’ ‘locfit’ ‘RColorBrewer’ ‘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’
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 : .local: no visible global function definition for
  ‘channelNames’
configure,cellHTS : .local: no visible global function definition for
  ‘notes<-’
configure,cellHTS : .local: no visible global function definition for
  ‘fData’
configure,cellHTS : .local: no visible global function definition for
  ‘fData<-’
configure,cellHTS : .local: no visible global function definition for
  ‘description<-’
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<-’
geneAnno,cellHTS: no visible global function definition for ‘fData’
initialize,cellHTS : .local: no visible binding for global variable
  ‘assayDataNew’
initialize,cellHTS : .local: no visible global function definition for
  ‘annotatedDataFrameFrom’
initialize,cellHTS : .local: no visible global function definition for
  ‘pData<-’
initialize,cellHTS : .local: no visible global function definition for
  ‘varMetadata<-’
initialize,cellHTS : .local: no visible global function definition for
  ‘varMetadata’
initialize,cellHTS : .local: no visible global function definition for
  ‘assayDataElementNames’
initialize,cellHTS : .local: no visible global function definition for
  ‘storageMode’
initialize,cellHTS : .local : <anonymous>: no visible global function
  definition for ‘sampleNames’
initialize,cellHTS : .local: no visible global function definition for
  ‘sampleNames<-’
initialize,cellHTS : .local: 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’
* 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 ... [62s/62s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
Bscore 5.66  0.041   5.709
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test.R’ [72s/75s]
 [73s/76s] 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-3.1-bioc/meat/cellHTS2.Rcheck/00check.log’
for details.

* installing *source* package ‘cellHTS2’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (cellHTS2)

name	user	system	elapsed
Bscore	5.660	0.041	5.709
ROC-class	0.542	0.014	0.658
ROC	2.339	0.011	2.354
annotate	1.975	0.007	1.984
bdgpbiomart	0.375	0.014	0.388
buildCellHTS2	1.035	0.022	1.057
cellHTS-class	2.605	0.071	2.678
configurationAsScreenPlot	3.421	0.034	3.459
configure	1.519	0.010	1.531
convertOldCellHTS	1.263	0.008	1.271
convertWellCoordinates	0.002	0.000	0.003
data-KcViab	0.211	0.014	0.225
data-KcViabSmall	0.018	0.009	0.027
data-dualCh	0.020	0.007	0.027
data-oldKcViabSmall	0.017	0.008	0.026
getDynamicRange	1.222	0.012	1.235
getEnVisionRawData	0.126	0.003	0.134
getMeasureRepAgreement	1.085	0.008	1.094
getTopTable	2.259	0.011	2.271
getZfactor	0.719	0.006	0.727
imageScreen	2.187	0.010	2.200
normalizePlates	2.487	0.011	2.499
oneRowPerId	0.005	0.000	0.006
plotSpatialEffects	3.235	0.020	3.256
readHTAnalystData	1.370	0.003	1.372
readPlateList	1.266	0.007	1.278
rsa	1.653	0.008	1.664
scoreReplicates	1.827	0.006	1.835
scores2calls	2.074	0.010	2.088
setSettings	0.009	0.003	0.012
spatialNormalization	2.123	0.011	2.138
summarizeChannels	3.609	0.007	3.616
summarizeReplicates	1.473	0.005	1.478
templateDescriptionFile	0.003	0.000	0.004
updateCellHTS	0.193	0.005	0.198
write.tabdel	0.094	0.005	0.100
writeReport	0.019	0.005	0.025
writeTab	0.026	0.006	0.032