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Package 122/233HostnameOS / ArchBUILDCHECKBUILD BIN
maDB 1.10.0
Johannes Rainer
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
Last Changed Rev: 27709 / Revision: 30966
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK [ OK ]
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64 N O T   S U P P O R T E D
lemming Windows Server 2003 (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 
Package: maDB
Version: 1.10.0
Command: /home/biocbuild/bbs-2.1-bioc/R/bin/R CMD check maDB_1.10.0.tar.gz
StartedAt: 2008-04-09 16:38:02 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 16:38:45 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 42.5 seconds
RetCode: 0
Status: OK
CheckDir: maDB.Rcheck
Warnings: 0

Command output

* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.1-bioc/meat/maDB.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'maDB/DESCRIPTION' ... OK
* this is package 'maDB' version '1.10.0'
* 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 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
dbGetGeneRegulationRanking: no visible global function definition for
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 =
.resetAfterError: no visible binding for global variable
* 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 ... NOTE
S3 methods shown with full name in documentation object 'format.latex':

S3 methods shown with full name in documentation object '':

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in manual 'Writing R
* checking data for non-ASCII characters ... OK
* creating maDB-Ex.R ... OK
* checking examples ... OK
* creating maDB-manual.tex ... OK
* checking maDB-manual.tex ... OK


* 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: affyio
Loading required package: preprocessCore
Loading required package: pgUtils
Loading required package: Rdbi
Loading required package: RdbiPgSQL

Attaching package: 'RdbiPgSQL'

	The following object(s) are masked from package:Rdbi :


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 
  EexprSet-class                    text    html    latex   example
  Layout-class                      text    html    latex   example
  MAtoG                             text    html    latex   example
  MAtoR                             text    html    latex   example
  MadbSet-class                     text    html    latex   example
  Sample-class                      text    html    latex   example
  SignalChannel-class               text    html    latex   example
  Similarity-class                  text    html    latex
  arrowProgress                     text    html    latex   example
  average                           text    html    latex
  calculateSimilarity               text    html    latex   example
  checkForAnnotation                text    html    latex   example
  createDirs                        text    html    latex   example
  createEexprSetFromLimma           text    html    latex   example
  createFile                        text    html    latex   example
  createJOINQuery                   text    html    latex   example
  createSampleFromTable             text    html    latex   example
  dbCalculateRegulations            text    html    latex
  dbGetComparisons                  text    html    latex
  dbGetGeneRegulationRanking        text    html    latex
  dbSearchSimilarPattern            text    html    latex   example
  deleteExperimentFromDB            text    html    latex
  distance.euclidian                text    html    latex   example
  distance.pearson                  text    html    latex   example
  distance.pearson.uncentered       text    html    latex   example
  distance.spearman                 text    html    latex   example
  drawMAPlot                        text    html    latex
  drawVolcanoPlot                   text    html    latex
  format.latex                      text    html    latex   example
  getAnnotation                     text    html    latex
  getDBAnnotation                   text    html    latex
  getExpValue                       text    html    latex
  getExperimentDBInfo               text    html    latex
  getMDB                            text    html    latex
  getPK                             text    html    latex   example
  getPathFromFile                   text    html    latex   example
  getSamplesFromDB                  text    html    latex
  isDecimal                         text    html    latex   example
  loadFromDB                        text    html    latex
  maDB-package                      text    html    latex
  mapply                            text    html    latex   example                       text    html    latex   example
  meanWithoutNA                     text    html    latex   example
  medianWithoutNA                   text    html    latex   example
  multiGrep                         text    html    latex   example
  myGrep                            text    html    latex   example
  newMadbSet                        text    html    latex
  openMadbVignette                  text    html    latex
  plotSimilarity                    text    html    latex
  progress                          text    html    latex   example
  publishToDB                       text    html    latex   example
  replaceAll                        text    html    latex   example
  replaces                          text    html    latex   example
  smallALL                          text    html    latex
  toEexprSet                        text    html    latex
  updateDBAnnotation                text    html    latex
  writeFigure                       text    html    latex   example
  writeLatexTable                   text    html    latex   example
** building package indices ...
* DONE (maDB)