Package: biomaRt

Version: 1.11.3

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check biomaRt_1.11.3.tar.gz

RetCode: 0

Time: 266.0 seconds

Status: WARNINGS

CheckDir: biomaRt.Rcheck

Warnings: 1

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/biomaRt.Rcheck'
* using R version 2.6.0 Under development (unstable) (2007-04-17 r41210)
* checking for file 'biomaRt/DESCRIPTION' ... OK
* this is package 'biomaRt' version '1.11.3'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'biomaRt' 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:
  RMySQL
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 ... 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 biomaRt-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating biomaRt-manual.tex ... OK
* checking biomaRt-manual.tex ... OK

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

* Installing *source* package 'biomaRt' ...
** R
** inst
** save image
Loading required package: XML
Loading required package: RCurl
** help
 >>> Building/Updating help pages for package 'biomaRt'
     Formats: text html latex example 
  Mart-class                        text    html    latex
  attributeSummary                  text    html    latex   example
  exportFASTA                       text    html    latex   example
  filterOptions                     text    html    latex   example
  filterSummary                     text    html    latex   example
  filterType                        text    html    latex   example
  getAffyArrays                     text    html    latex   example
  getBM                             text    html    latex   example
  getFeature                        text    html    latex   example
  getGO                             text    html    latex   example
  getGene                           text    html    latex   example
  getHomolog                        text    html    latex   example
  getLDS                            text    html    latex   example
  getSNP                            text    html    latex   example
  getSequence                       text    html    latex   example
  listAttributes                    text    html    latex   example
  listDatasets                      text    html    latex   example
  listFilters                       text    html    latex   example
  listMarts                         text    html    latex   example
  martDisconnect                    text    html    latex   example
  parseAttributes                   text    html    latex
  parseFilters                      text    html    latex
  useDataset                        text    html    latex   example
  useMart                           text    html    latex   example
** building package indices ...
* DONE (biomaRt)