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BioC 3.0: CHECK report for cellHTS2 on moscato1

This page was generated on 2015-04-10 09:44:54 -0700 (Fri, 10 Apr 2015).

Package 131/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cellHTS2 2.30.0
Joseph Barry
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/cellHTS2
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: cellHTS2
Version: 2.30.0
Command: rm -rf cellHTS2.buildbin-libdir cellHTS2.Rcheck && mkdir cellHTS2.buildbin-libdir cellHTS2.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.30.0.tar.gz >cellHTS2.Rcheck\00install.out 2>&1 && cp cellHTS2.Rcheck\00install.out cellHTS2-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.30.0.tar.gz
StartedAt: 2015-04-09 23:25:15 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:35:58 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 643.0 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cellHTS2.buildbin-libdir cellHTS2_2.30.0.tar.gz >cellHTS2.Rcheck\00install.out 2>&1 && cp cellHTS2.Rcheck\00install.out cellHTS2-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=cellHTS2.buildbin-libdir --install="check:cellHTS2-install.out" --force-multiarch --no-vignettes --timings cellHTS2_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/cellHTS2.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellHTS2/DESCRIPTION' ... OK
* this is package 'cellHTS2' version '2.30.0'
* 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  5.7Mb
  sub-directories of 1Mb or more:
    KcViab   2.0Mb
    doc      1.7Mb
* 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
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'
geneAnno,cellHTS: no visible global function definition for 'fData'
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [46s] OK
** running examples for arch 'x64' ... [59s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test.R' [68s]
 [68s] OK
** running tests for arch 'x64' ...
  Running 'test.R' [68s]
 [69s] 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

NOTE: There were 5 notes.
See
  'D:/biocbld/bbs-3.0-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_2.30.0.zip
* DONE (cellHTS2)

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

nameusersystemelapsed
Bscore3.730.013.74
ROC-class0.320.000.33
ROC1.470.001.46
annotate1.170.021.19
bdgpbiomart0.220.000.22
buildCellHTS20.370.000.37
cellHTS-class1.840.001.84
configurationAsScreenPlot202
configure0.760.010.78
convertOldCellHTS0.830.000.83
convertWellCoordinates000
data-KcViab0.170.000.17
data-KcViabSmall0.020.000.01
data-dualCh0.010.000.02
data-oldKcViabSmall000
getDynamicRange0.700.000.71
getEnVisionRawData0.050.000.04
getMeasureRepAgreement0.580.000.58
getTopTable1.560.001.56
getZfactor0.430.000.44
imageScreen1.310.021.32
normalizePlates2.060.002.06
oneRowPerId000
plotSpatialEffects2.140.002.16
readHTAnalystData1.040.021.06
readPlateList0.720.010.79
rsa1.560.001.56
scoreReplicates1.310.001.31
scores2calls1.390.001.91
setSettings000
spatialNormalization1.420.021.43
summarizeChannels2.340.002.34
summarizeReplicates1.120.001.12
templateDescriptionFile000
updateCellHTS0.100.010.11
write.tabdel0.050.000.05
writeReport000
writeTab0.010.020.03

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

nameusersystemelapsed
Bscore4.290.034.32
ROC-class0.360.020.38
ROC2.480.002.48
annotate1.570.001.57
bdgpbiomart0.350.000.35
buildCellHTS20.740.000.73
cellHTS-class2.600.002.61
configurationAsScreenPlot2.110.012.12
configure1.010.001.02
convertOldCellHTS1.080.001.07
convertWellCoordinates000
data-KcViab0.140.000.14
data-KcViabSmall0.020.000.01
data-dualCh0.010.000.02
data-oldKcViabSmall0.000.020.01
getDynamicRange0.890.010.91
getEnVisionRawData0.030.020.05
getMeasureRepAgreement0.690.010.70
getTopTable1.940.001.95
getZfactor0.560.020.58
imageScreen1.810.001.80
normalizePlates2.340.002.34
oneRowPerId0.010.000.02
plotSpatialEffects2.790.002.79
readHTAnalystData1.140.001.14
readPlateList0.940.011.02
rsa1.260.001.26
scoreReplicates1.370.001.38
scores2calls1.730.001.73
setSettings000
spatialNormalization1.590.001.59
summarizeChannels3.300.003.29
summarizeReplicates1.850.001.86
templateDescriptionFile000
updateCellHTS0.250.000.25
write.tabdel0.110.000.11
writeReport0.020.020.03
writeTab0.030.000.03