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Package 92/251HostnameOS / ArchBUILDCHECKBUILD BIN
GEOquery 2.3.0
Sean Davis
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GEOquery
Last Changed Rev: 28557 / Revision: 29143
Last Changed Date: 2007-11-07 23:00:31 -0800 (Wed, 07 Nov 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK [ ERROR ] OK 
Package: GEOquery
Version: 2.3.0
Command: D:\biocbld\bbs-2.2-bioc\R\bin\R.exe CMD check GEOquery_2.3.0.tar.gz
StartedAt: 2007-12-11 06:19:59 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 06:22:00 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 121.5 seconds
RetCode: 1
Status: ERROR
CheckDir: GEOquery.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.2-bioc/meat/GEOquery.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'GEOquery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GEOquery' version '2.3.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GEOquery' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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 ... 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating GEOquery-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'GEOquery-Ex.R' failed.
The error most likely occurred in:

> ### * getGEOfile
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: getGEOfile
> ### Title: Download a file from GEO soft file to the local machine
> ### Aliases: getGEOfile
> ### Keywords: IO
> 
> ### ** Examples
> 
>   myfile <- getGEOfile('GDS2')
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS2.soft.gz'
Error in download.file(myurl, destfile, mode = mode) : 
  cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS2.soft.gz'
Calls: getGEOfile -> download.file
Execution halted

GEOquery.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.2-bioc/meat/GEOquery.Rcheck


---------- Making package GEOquery ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing man source files
  installing indices
  installing help
Note: removing empty section \usage
Note: removing empty section \details
Note: removing empty section \arguments
Note: removing empty section \usage
Note: removing empty section \details
Note: removing empty section \arguments
 >>> Building/Updating help pages for package 'GEOquery'
     Formats: text html latex example chm 
  GDS-class                         text    html    latex           chm
  GDS2MA                            text    html    latex   example chm
  GEOData-class                     text    html    latex           chm
  GEODataTable-class                text    html    latex           chm
  GPL-class                         text    html    latex           chm
  GSE-class                         text    html    latex           chm
  GSM-class                         text    html    latex           chm
  dataTable                         text    html    latex           chm
  getGEO                            text    html    latex   example chm
  getGEOfile                        text    html    latex   example chm
  gunzip                            text    html    latex           chm
  parseGEO                          text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.2-bioc\meat\GEOquery.Rcheck\00_pkg_src\GEOquery\chm\GEOquery.chm


Compile time: 0 minutes, 1 second
13	Topics
63	Local links
1	Internet link
1	Graphic


Created d:\biocbld\bbs-2.2-bioc\meat\GEOquery.Rcheck\00_pkg_src\GEOquery\chm\GEOquery.chm, 30,599 bytes
Compression decreased file by 13,623 bytes.
  adding MD5 sums

* DONE (GEOquery)