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Package 177/208OSArchBUILDCHECKBUILD BIN

SAGElyzer

1.13.0

Jianhua Zhang
Linux (SUSE 9.2) x86_64 OK [ WARNINGS ]
Linux (SUSE 10.1) x86_64 OK  WARNINGS 
Linux (SUSE 9.2) i686 OK  WARNINGS 
Solaris 2.9 sparc OK  WARNINGS 
Windows Server 2003 x86_64 OK  ERROR  OK 
Windows Server 2003 NA OK  ERROR  OK 
Mac OS X (10.4.6) i686 OK  ERROR 
Package: SAGElyzer
Version: 1.13.0
Command: /loc/biocbuild/2.0d/R/bin/R CMD check SAGElyzer_1.13.0.tar.gz
RetCode: 0
Time: 89.9 seconds
Status: WARNINGS
CheckDir: SAGElyzer.Rcheck
Warnings: 2

Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/2.0d/Rpacks/SAGElyzer.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'SAGElyzer/DESCRIPTION' ... OK
* this is package 'SAGElyzer' version '1.13.0'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  RODBC Rdbi RdbiPgSQL Biobase
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 '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 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 whether the name space 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 ... WARNING
Undocumented code objects:
  findNG4Tag getBinding getDBArgs getLibCounts getSAGEKNN getSLyzerArgs
  getTag getUnixDBArgs getWinDBArgs linkTag2UG mapLib2File mapSAGE2UG
  modSLyzerArgs procSAGE remapTagNUG runSLyzer SAGEFromGEO setKNNArgs
  setSLyzerArgs showDBError writeSAGEKNN writeSLyzerArgs
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 were 2 warnings, see
  /loc/biocbuild/2.0d/Rpacks/SAGElyzer.Rcheck/00check.log
for details

SAGElyzer.Rcheck/00install.out:

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

Loading required package: XML
Loading required package: annotate
Loading required package: tkWidgets
Loading required package: widgetTools
Loading Tcl/Tk interface ... done
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
** building package indices ...
* DONE (SAGElyzer)