Package: SAGElyzer

Version: 1.16.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check SAGElyzer_1.16.0.tar.gz

RetCode: 0

Time: 156.7 seconds

Status: WARNINGS

CheckDir: SAGElyzer.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/SAGElyzer.Rcheck'
* using R version 2.6.0 (2007-10-03)
* checking for file 'SAGElyzer/DESCRIPTION' ... OK
* this is package 'SAGElyzer' version '1.16.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'SAGElyzer' 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 ... WARNING
'library' or 'require' calls not declared from:
  RODBC Rdbi RdbiPgSQL
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
closeConn: no visible global function definition for 'odbcClose'
con4Win: no visible global function definition for 'odbcConnect'
executeQuery: no visible global function definition for 'sqlQuery'
tableExists: no visible global function definition for
  'odbcTableExists'
writeSAGE2DB: no visible global function definition for 'sqlSave'
writeSAGE4Win: no visible global function definition for 'sqlSave'
* 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 SAGElyzer-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating SAGElyzer-manual.tex ... OK
* checking SAGElyzer-manual.tex ... OK

WARNING: There was 1 warning, see
  /extra/loc/biocbuild/bbs-2.1-bioc/meat/SAGElyzer.Rcheck/00check.log
for details

* Installing *source* package 'SAGElyzer' ...
** R
** data
** exec
** inst
** preparing package for lazy loading
Loading required package: AnnBuilder
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: XML
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: tkWidgets
Loading required package: widgetTools
Loading required package: tcltk
Loading Tcl/Tk interface ... done

Attaching package: 'widgetTools'


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

	 label 

Loading required package: DynDoc
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
** help
 >>> Building/Updating help pages for package 'SAGElyzer'
     Formats: text html latex example 
  SAGELyzer                         text    html    latex   example
  SAGEMapper                        text    html    latex   example
  SAGEToolTips                      text    html    latex   example
  SAGEWidget                        text    html    latex   example
  con4Win                           text    html    latex   example
  getGEOSAGE                        text    html    latex   example
  getNormFactor                     text    html    latex   example
  getTargetRow                      text    html    latex   example
  mergeSAGE                         text    html    latex   example
  mergeSAGEWidget                   text    html    latex   example
  querySAGE                         text    html    latex   example
  support                           text    html    latex   example
** building package indices ...
* DONE (SAGElyzer)