[BioC] GEOmetadb: problem with SQLite database download

[axel.klenk at actelion.com]

Dear BioC list,

I have tried updating my GEOmetadb SQLite database today
using the code below (which has worked for me about a month
ago) and received the following error message:

> library("GEOmetadb")
Loading required package: GEOquery
Loading required package: RCurl
Loading required package: bitops
Loading required package: RSQLite
Loading required package: DBI

> getSQLiteFile()
trying URL 'http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz'
Error in download.file("
http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz",  : 
  cannot open URL 'http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz'
In addition: Warning message:
In download.file("http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz", 
:
  cannot open: HTTP status was '404 Not Found'


In addition, the package website at http://gbnci.abcc.ncifcrf.gov/geo/
reports a funny size and date for this file -- and the link to that file 
also 
gives an HTTP 404. So I assume there's a problem on the server side
or am I going wrong somewhere?

Thanks in advance, 

 - axel 


> sessionInfo()
R version 2.10.1 (2009-12-14) 
x86_64-pc-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C 
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8 
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8 
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C 
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base 

other attached packages:
 [1] GEOmetadb_1.6.0     RSQLite_0.7-3       DBI_0.2-4 
 [4] GEOquery_2.11.2     RCurl_1.3-0         bitops_1.0-4.1 
 [7] limma_3.2.1         sfsmisc_1.0-9       geneplotter_1.24.0 
[10] lattice_0.17-26     annotate_1.24.0     AnnotationDbi_1.8.1
[13] Biobase_2.6.1       MASS_7.3-3          gmodels_2.15.0 
[16] fortunes_1.3-6 

loaded via a namespace (and not attached):
[1] gdata_2.6.1        grid_2.10.1        gtools_2.6.1 RColorBrewer_1.0-2
[5] tools_2.10.1       xtable_1.5-6 


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland



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