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GEOquery

1.7.3

Sean Davis		Linux (SUSE 9.2) x86_64 OK  WARNINGS 
Linux (SUSE 9.2) i686 OK  WARNINGS 
Solaris 2.9 sparc OK [ WARNINGS ]
Linux (SUSE 10.0) x86_64 OK  WARNINGS 
Windows Server 2003 x86_64 OK  WARNINGS  OK 
Windows XP i686 OK  WARNINGS skipped
Mac OS X (10.4.6) i686 OK  WARNINGS 
Package: GEOquery
Version: 1.7.3
Command: /loc/biocbuild/1.9d/R/bin/R CMD check GEOquery_1.7.3.tar.gz
RetCode: 0
Time: 257.0 seconds
Status: WARNINGS
CheckDir: GEOquery.Rcheck
Warnings: 3

Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/1.9d/Rpacks/GEOquery.Rcheck'
* using R version 2.4.0 Under development (unstable) (2006-07-18 r38641)
* 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 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 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 3 warnings, see
  /loc/biocbuild/1.9d/Rpacks/GEOquery.Rcheck/00check.log
for details

GEOquery.Rcheck/00install.out:

* 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)