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Package 58/319HostnameOS / ArchBUILDCHECKBUILD BIN
cellHTS2 2.8.3
Florian Hahne
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/cellHTS2
Last Changed Rev: 40951 / Revision: 42512
Last Changed Date: 2009-08-01 10:06:58 -0700 (Sat, 01 Aug 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 
Package: cellHTS2
Version: 2.8.3
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes cellHTS2_2.8.3.tar.gz
StartedAt: 2009-10-20 17:13:00 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 17:17:15 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 255.2 seconds
RetCode: 0
Status: OK
CheckDir: cellHTS2.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/cellHTS2.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cellHTS2/DESCRIPTION' ... OK
* this is package 'cellHTS2' version '2.8.3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'cellHTS2' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
chanCorrFun: no visible binding for global variable ‘nrChannel’
chanCorrFun: no visible binding for global variable ‘maxRep’
chanCorrFun: no visible binding for global variable ‘isTwoWay’
chanCorrFun: no visible binding for global variable ‘pact’
chanCorrFun: no visible binding for global variable ‘pinh’
chanCorrFun: no visible binding for global variable ‘pneg’
chanCorrFun: no visible binding for global variable ‘ppos’
chanCorrFun: no visible binding for global variable ‘wellTypeColor’
chanCorrFun: no visible binding for global variable ‘mt’
chanCorrFun: no visible binding for global variable ‘finalWellAnno’
chanCorrFun: no visible binding for global variable ‘iwells’
chanCorrFun: no visible binding for global variable ‘whHasData’
chanCorrFun: no visible binding for global variable ‘basePath’
chanCorrFun: no visible binding for global variable ‘subPath’
chanCorrFun: no visible binding for global variable ‘con’
chanCorrFun: no visible binding for global variable ‘plsiz’
chanCorrFun : <anonymous>: no visible binding for global variable
  ‘platedat’
chanCorrFun : <anonymous>: no visible binding for global variable
  ‘wellTypeColor’
corrFun: no visible binding for global variable ‘nrChannel’
corrFun: no visible binding for global variable ‘nrRepCh’
corrFun: no visible binding for global variable ‘qmsummary’
corrFun: no visible binding for global variable ‘wellCount’
corrFun: no visible binding for global variable ‘basePath’
corrFun: no visible binding for global variable ‘subPath’
corrFun: no visible binding for global variable ‘con’
corrFun: no visible binding for global variable ‘plsiz’
corrFun : <anonymous>: no visible binding for global variable
  ‘platedat’
corrFun : <anonymous>: no visible binding for global variable
  ‘whHasData’
corrFun : <anonymous>: no visible binding for global variable
  ‘wellTypeColor’
corrFun : <anonymous>: no visible binding for global variable ‘mtt’
corrFun: no visible binding for global variable ‘platedat’
corrFun: no visible binding for global variable ‘whHasData’
histFun: no visible binding for global variable ‘nrChannel’
histFun: no visible binding for global variable ‘nrRepCh’
histFun: no visible binding for global variable ‘maxRep’
histFun: no visible binding for global variable ‘iwells’
histFun: no visible binding for global variable ‘whHasData’
histFun: no visible binding for global variable ‘basePath’
histFun: no visible binding for global variable ‘subPath’
histFun: no visible binding for global variable ‘con’
histFun: no visible binding for global variable ‘plsiz’
histFun : <anonymous>: no visible binding for global variable
  ‘platedat’
histFun : <anonymous>: no visible binding for global variable ‘brks’
histFun : <anonymous>: no visible binding for global variable ‘mtt’
histFun : <anonymous>: no visible binding for global variable
  ‘wellTypeColor’
histFun: no visible binding for global variable ‘qmsummary’
intensFun: no visible binding for global variable ‘nrChannel’
intensFun: no visible binding for global variable ‘platedat’
intensFun: no visible binding for global variable ‘pneg’
intensFun: no visible binding for global variable ‘isTwoWay’
intensFun: no visible binding for global variable ‘pact’
intensFun: no visible binding for global variable ‘pinh’
intensFun: no visible binding for global variable ‘ppos’
intensFun: no visible binding for global variable ‘maxRep’
intensFun: no visible binding for global variable ‘whHasData’
intensFun: no visible binding for global variable ‘basePath’
intensFun: no visible binding for global variable ‘subPath’
intensFun: no visible binding for global variable ‘con’
intensFun: no visible binding for global variable ‘plsiz’
intensFun : <anonymous>: no visible binding for global variable
  ‘platedat’
intensFun: no visible binding for global variable ‘genAnno’
sdFun: no visible binding for global variable ‘nrChannel’
sdFun: no visible binding for global variable ‘platedat’
sdFun: no visible binding for global variable ‘pneg’
sdFun: no visible binding for global variable ‘isTwoWay’
sdFun: no visible binding for global variable ‘pact’
sdFun: no visible binding for global variable ‘pinh’
sdFun: no visible binding for global variable ‘ppos’
sdFun: no visible binding for global variable ‘qmsummary’
sdFun: no visible binding for global variable ‘basePath’
sdFun: no visible binding for global variable ‘subPath’
sdFun: no visible binding for global variable ‘con’
sdFun: no visible binding for global variable ‘plsiz’
sdFun: no visible binding for global variable ‘genAnno’
Data<-,cellHTS-array: no visible global function definition for
  ‘channelNames<-’
* checking Rd files ... OK
* checking Rd files against version 2 parser ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

cellHTS2.Rcheck/00install.out:

* Installing *source* package ‘cellHTS2’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: grid
Scalable Robust Estimators with High Breakdown Point (version 1.0-00)
Creating a new generic function for "lines" in "cellHTS2"
** help
*** installing help indices
 >>> Building/Updating help pages for package 'cellHTS2'
     Formats: text html latex example 
  Bscore                            text    html    latex   example
  Data                              text    html    latex
  ROC-class                         text    html    latex   example
  ROC                               text    html    latex   example
  annotate                          text    html    latex   example
  batch                             text    html    latex
  bdgpbiomart                       text    html    latex   example
  cellHTS-class                     text    html    latex   example
  cellHTS2                          text    html    latex
  configurationAsScreenPlot         text    html    latex   example
  configure                         text    html    latex   example
  convertOldCellHTS                 text    html    latex   example
  convertWellCoordinates            text    html    latex   example
  data-KcViab                       text    html    latex   example
  data-KcViabSmall                  text    html    latex   example
  data-dualCh                       text    html    latex   example
  data-oldKcViabSmall               text    html    latex   example
  getDynamicRange                   text    html    latex   example
  getEnVisionRawData                text    html    latex   example
  getMeasureRepAgreement            text    html    latex   example
  getTopTable                       text    html    latex   example
  getZfactor                        text    html    latex   example
  imageScreen                       text    html    latex   example
  intensityFiles                    text    html    latex
  normalizePlates                   text    html    latex   example
  oneRowPerId                       text    html    latex   example
  plate                             text    html    latex
  plateEffects                      text    html    latex
  plotSpatialEffects                text    html    latex   example
  readHTAnalystData                 text    html    latex   example
  readPlateList                     text    html    latex   example
  scoreReplicates                   text    html    latex   example
  scores2calls                      text    html    latex   example
  spatialNormalization              text    html    latex   example
  state                             text    html    latex
  summarizeChannels                 text    html    latex   example
  summarizeReplicates               text    html    latex   example
  templateDescriptionFile           text    html    latex   example
  updateCellHTS                     text    html    latex   example
  wellAnno                          text    html    latex
  write.tabdel                      text    html    latex   example
  writeReport                       text    html    latex   example
  writeTab                          text    html    latex   example
** building package indices ...
* DONE (cellHTS2)