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Package 160/294HostnameOS / ArchBUILDCHECKBUILD BIN
maDB 1.14.1
Johannes Rainer
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/maDB
Last Changed Rev: 35895 / Revision: 38965
Last Changed Date: 2008-12-12 01:59:33 -0800 (Fri, 12 Dec 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64 N O T   S U P P O R T E D
pitt Mac OS X Tiger (10.4.11) / i386  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK  OK  OK 
Package: maDB
Version: 1.14.1
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes maDB_1.14.1.tar.gz
StartedAt: 2009-04-18 17:16:28 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 17:17:47 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 79.5 seconds
RetCode: 0
Status: OK
CheckDir: maDB.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/maDB.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'maDB/DESCRIPTION' ... OK
* this is package 'maDB' version '1.14.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'maDB' 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
.calcRegulations: no visible binding for global variable 'con'
.calculateDBRegulations.old: no visible binding for global variable
  'con'
.resetAfterError: no visible binding for global variable
  'ConnectionForErrors'
dbGetGeneRegulationRanking: no visible global function definition for
  'getDBAnnotation'
getAnnotation: possible error in dbGetAnnotation(con = con, id = id, v
  = v, chip = chip, ...): unused argument(s) (con = con)
getAnnotation: possible error in getGene(mart = con, id = id, array =
  .toMartChip(chip), ...): unused argument(s) (array =
  .toMartChip(chip))
drawMA,exprSet: no visible binding for global variable 'main...'
loadFromDB,EexprSet: no visible binding for global variable 'con'
loadFromDB,MadbSet: no visible binding for global variable 'con'
* checking Rd files ... 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
* creating maDB-Ex.R ... OK
* checking examples ... OK
* creating maDB-manual.tex ... OK
* checking maDB-manual.tex using pdflatex ... OK

maDB.Rcheck/00install.out:

* Installing *source* package 'maDB' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

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: affy
Loading required package: pgUtils
Loading required package: Rdbi
Loading required package: RdbiPgSQL
Loading required package: limma
Creating a new generic function for "sort" in "maDB"
** help
 >>> Building/Updating help pages for package 'maDB'
     Formats: text html latex example 
Note: removing empty section \note in file 'EexprSet-class.Rd'
Note: removing empty section \examples in file 'EexprSet-class.Rd'
  EexprSet-class                    text    html    latex
Note: removing empty section \references in file 'Layout-class.Rd'
Note: removing empty section \examples in file 'Layout-class.Rd'
  Layout-class                      text    html    latex
Note: removing empty section \references in file 'MAtoG.Rd'
Note: removing empty section \examples in file 'MAtoG.Rd'
  MAtoG                             text    html    latex
Note: removing empty section \references in file 'MAtoR.Rd'
Note: removing empty section \examples in file 'MAtoR.Rd'
  MAtoR                             text    html    latex
Note: removing empty section \examples in file 'MadbSet-class.Rd'
  MadbSet-class                     text    html    latex
Note: removing empty section \references in file 'Sample-class.Rd'
Note: removing empty section \examples in file 'Sample-class.Rd'
  Sample-class                      text    html    latex
Note: removing empty section \references in file 'SignalChannel-class.Rd'
Note: removing empty section \examples in file 'SignalChannel-class.Rd'
  SignalChannel-class               text    html    latex
  Similarity-class                  text    html    latex
Note: removing empty section \references in file 'arrowProgress.Rd'
  arrowProgress                     text    html    latex   example
Note: removing empty section \references in file 'average.Rd'
  average                           text    html    latex
Note: removing empty section \references in file 'calculateSimilarity.Rd'
  calculateSimilarity               text    html    latex   example
Note: removing empty section \references in file 'checkForAnnotation.Rd'
Note: removing empty section \examples in file 'checkForAnnotation.Rd'
  checkForAnnotation                text    html    latex
Note: removing empty section \references in file 'createDirs.Rd'
Note: removing empty section \examples in file 'createDirs.Rd'
  createDirs                        text    html    latex
Note: removing empty section \references in file 'createEexprSetFromLimma.Rd'
Note: removing empty section \examples in file 'createEexprSetFromLimma.Rd'
  createEexprSetFromLimma           text    html    latex
Note: removing empty section \references in file 'createFile.Rd'
Note: removing empty section \examples in file 'createFile.Rd'
  createFile                        text    html    latex
  createJOINQuery                   text    html    latex   example
Note: removing empty section \references in file 'createSampleFromTable.Rd'
Note: removing empty section \examples in file 'createSampleFromTable.Rd'
  createSampleFromTable             text    html    latex
Note: removing empty section \references in file 'dbCalculateRegulations.Rd'
  dbCalculateRegulations            text    html    latex
  dbGetComparisons                  text    html    latex
  dbGetGeneRegulationRanking        text    html    latex
Note: removing empty section \references in file 'dbSearchSimilarPattern.Rd'
Note: removing empty section \examples in file 'dbSearchSimilarPattern.Rd'
  dbSearchSimilarPattern            text    html    latex
Note: removing empty section \references in file 'deleteExperimentFromDB.Rd'
  deleteExperimentFromDB            text    html    latex
Note: removing empty section \references in file 'distance.euclidian.Rd'
Note: removing empty section \examples in file 'distance.euclidian.Rd'
  distance.euclidian                text    html    latex
Note: removing empty section \references in file 'distance.pearson.Rd'
Note: removing empty section \examples in file 'distance.pearson.Rd'
  distance.pearson                  text    html    latex
Note: removing empty section \references in file 'distance.pearson.uncentered.Rd'
Note: removing empty section \examples in file 'distance.pearson.uncentered.Rd'
  distance.pearson.uncentered       text    html    latex
Note: removing empty section \references in file 'distance.spearman.Rd'
Note: removing empty section \examples in file 'distance.spearman.Rd'
  distance.spearman                 text    html    latex
  drawMAPlot                        text    html    latex
Note: removing empty section \references in file 'drawVolcanoPlot.Rd'
  drawVolcanoPlot                   text    html    latex
Note: removing empty section \references in file 'format.latex.Rd'
Note: removing empty section \seealso in file 'format.latex.Rd'
Note: removing empty section \examples in file 'format.latex.Rd'
  format.latex                      text    html    latex
  getAnnotation                     text    html    latex
Note: removing empty section \references in file 'getDBAnnotation.Rd'
  getDBAnnotation                   text    html    latex
Note: removing empty section \references in file 'getExpValue.Rd'
  getExpValue                       text    html    latex
Note: removing empty section \references in file 'getExperimentDBInfo.Rd'
  getExperimentDBInfo               text    html    latex
Note: removing empty section \details in file 'getMDB.Rd'
Note: removing empty section \references in file 'getMDB.Rd'
  getMDB                            text    html    latex
Note: removing empty section \examples in file 'getPK.Rd'
  getPK                             text    html    latex
Note: removing empty section \details in file 'getPathFromFile.Rd'
Note: removing empty section \references in file 'getPathFromFile.Rd'
  getPathFromFile                   text    html    latex   example
Note: removing empty section \references in file 'getSamplesFromDB.Rd'
  getSamplesFromDB                  text    html    latex
Note: removing empty section \references in file 'isDecimal.Rd'
Note: removing empty section \seealso in file 'isDecimal.Rd'
  isDecimal                         text    html    latex   example
  loadFromDB                        text    html    latex
  maDB-package                      text    html    latex
Note: removing empty section \references in file 'mapply.Rd'
  mapply                            text    html    latex   example
Note: removing empty section \references in file 'mean.center.Rd'
  mean.center                       text    html    latex   example
Note: removing empty section \references in file 'meanWithoutNA.Rd'
  meanWithoutNA                     text    html    latex   example
Note: removing empty section \references in file 'medianWithoutNA.Rd'
  medianWithoutNA                   text    html    latex   example
Note: removing empty section \references in file 'multiGrep.Rd'
  multiGrep                         text    html    latex   example
Note: removing empty section \references in file 'myGrep.Rd'
Note: removing empty section \examples in file 'myGrep.Rd'
  myGrep                            text    html    latex
  newMadbSet                        text    html    latex
  openMadbVignette                  text    html    latex
  plotSimilarity                    text    html    latex
Note: removing empty section \references in file 'progress.Rd'
  progress                          text    html    latex   example
Note: removing empty section \details in file 'publishToDB.Rd'
Note: removing empty section \references in file 'publishToDB.Rd'
Note: removing empty section \examples in file 'publishToDB.Rd'
  publishToDB                       text    html    latex
Note: removing empty section \references in file 'replaceAll.Rd'
  replaceAll                        text    html    latex   example
Note: removing empty section \references in file 'replaces.Rd'
  replaces                          text    html    latex   example
  smallALL                          text    html    latex
  toEexprSet                        text    html    latex
Note: removing empty section \references in file 'updateDBAnnotation.Rd'
  updateDBAnnotation                text    html    latex
Note: removing empty section \references in file 'writeFigure.Rd'
Note: removing empty section \examples in file 'writeFigure.Rd'
  writeFigure                       text    html    latex
Note: removing empty section \references in file 'writeLatexTable.Rd'
Note: removing empty section \examples in file 'writeLatexTable.Rd'
  writeLatexTable                   text    html    latex
** building package indices ...
* DONE (maDB)