[BioC] GEOmetadb: problem with SQLite database download

[axel.klenk at actelion.com]

Hi Jack and Sean,

yep, it works again -- thanks a lot for your quick help,

 - axel


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




Jack Zhu <zhujack at mail.nih.gov> 
Sent by: yuelin at gmail.com
12/16/2009 04:42 PM

To
axel.klenk at actelion.com
cc
"Davis, Sean (NCI)" <seandavi at gmail.com>
Subject
Re: [BioC] GEOmetadb: problem with SQLite database download






Hi Axel,

GEOmetadb.sqlite.gz was not available due to one of our servers was
down.  It has been fixed.  Thanks for the message.

Jack


On Wed, Dec 16, 2009 at 10:19 AM, Davis, Sean (NCI) <seandavi at gmail.com> 
wrote:
> I assume this was due to Alps being down.  Can you trigger a build?
>
> Thanks,
> Sean
>
>
> ---------- Forwarded message ----------
> From:  <axel.klenk at actelion.com>
> Date: Wed, Dec 16, 2009 at 9:43 AM
> Subject: [BioC] GEOmetadb: problem with SQLite database download
> To: bioconductor at stat.math.ethz.ch
>
>
> 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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