Package: GEOquery

Version: 1.7.3

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check GEOquery_1.7.3.tar.gz

RetCode: 0

Time: 140.1 seconds

Status: WARNINGS

CheckDir: GEOquery.Rcheck

Warnings: 4

* checking for working latex ... OK
* using log directory '/Users/biocbuild/1.9d/Rpacks/GEOquery.Rcheck'
* using R version 2.4.0 alpha (2006-09-07 r39185)
* checking for file 'GEOquery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOquery' version '1.7.3'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GEOquery' can be installed ... WARNING
Found the following significant warnings:
       missing link(s):  dataTable-class
* 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 ... WARNING
Error in eval(expr, envir, enclos) : could not find function "setClass"
Error: unable to load R code in package 'GEOquery'
Execution halted

A namespace must be able to be loaded with just the base namespace loaded:
otherwise if the namespace gets loaded by a saved object, the session will
be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 ... WARNING
Missing link(s) in documentation object 'GEOData-class.Rd':
  dataTable-class

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  Accession Columns GPLList GSMList Meta Table dataTable
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 GEOquery-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating GEOquery-manual.tex ... OK
* checking GEOquery-manual.tex ... OK

WARNING: There were 4 warnings, see
  /Users/biocbuild/1.9d/Rpacks/GEOquery.Rcheck/00check.log
for details

* Installing *source* package 'GEOquery' ...
** R
** inst
** help
 >>> Building/Updating help pages for package 'GEOquery'
     Formats: text html latex example 
  GDS-class                         text    html    latex
  GDS2MA                            text    html    latex   example
  GEOData-class                     text    html    latex
     missing link(s):  dataTable-class
  GEODataTable-class                text    html    latex
  GPL-class                         text    html    latex
  GSE-class                         text    html    latex
  GSM-class                         text    html    latex
  getGEO                            text    html    latex   example
  getGEOfile                        text    html    latex   example
  parseGEO                          text    html    latex
** building package indices ...
* DONE (GEOquery)