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GEOquery 2.2.0
Sean Davis
Last Changed Date: 2007-10-02 17:41:09 -0700
Last Changed Rev: 27709
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686 [ ERROR ]skipped
liverpool Windows Server 2003 R2 (32-bit) x64  OK  OK  OK 
pitt Mac OS X (10.4.10) i386  ERROR skippedskipped
Package: GEOquery
Version: 2.2.0
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build GEOquery
RetCode: 1
Time: 223.3 seconds
Status: ERROR
PackageFile: None

Command output

* checking for file 'GEOquery/DESCRIPTION' ... OK
* preparing 'GEOquery':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* 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
  GEODataTable-class                text    html    latex
  GPL-class                         text    html    latex
  GSE-class                         text    html    latex
  GSM-class                         text    html    latex
  dataTable                         text    html    latex
  getGEO                            text    html    latex   example
  getGEOfile                        text    html    latex   example
  gunzip                            text    html    latex
  parseGEO                          text    html    latex
** building package indices ...
* DONE (GEOquery)
* creating vignettes ... ERROR
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: RCurl
trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz'
ftp data connection made, file length 162427 bytes
opened URL
==================================================
downloaded 158 Kb

trying URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GSM3&form=text&view=full'
Content type 'geo/text' length unknown
opened URL
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... .......... .......... .......... ..........
.......... ...
downloaded 213 Kb

trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE462/GSE462_family.soft.gz'
ftp data connection made, file length 550629 bytes
opened URL
==================================================
downloaded 537 Kb


Error: processing vignette 'GEOquery.Rnw' failed with diagnostics:
 chunk 7 
Error in curlPerform(curl = curl, .opts = opts) : 
  Connect failed; Operation now in progress
Execution halted