Package: maDB

Version: 1.7.3

Command: /loc/biocbuild/2.0d/R/bin/R CMD check maDB_1.7.3.tar.gz

RetCode: 0

Time: 135.3 seconds

Status: WARNINGS

CheckDir: maDB.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/loc/biocbuild/2.0d/Rpacks/maDB.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'maDB/DESCRIPTION' ... OK
* this is package 'maDB' version '1.7.3'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  annaffy biomaRt
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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
* creating maDB-Ex.R ... OK
* checking examples ... OK
* creating maDB-manual.tex ... OK
* checking maDB-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/biocbuild/2.0d/Rpacks/maDB.Rcheck/00check.log
for details

* 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()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affy
Loading required package: affyio
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
  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
  mapply                            text    html    latex   example
  mean.center                       text    html    latex   example
  meanWithoutNA                     text    html    latex   example
  medianWithoutNA                   text    html    latex   example
  multiGrep                         text    html    latex   example
  myGrep                            text    html    latex   example
  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)