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Question: Cannot download GEOmetadb sqlite file
1
gravatar for arnaud.ceol.pro
11 days ago by
arnaud.ceol.pro10 wrote:

Hi, 

I cannot download the sqlite file anymore:

> getSQLiteFile(destdir=geoDbPath)
trying URL 'http://watson.nci.nih.gov/~zhujack/GEOmetadb.sqlite.gz'
Error in download.file(url_geo, destfile = localfile, mode = "wb") :
  cannot open URL 'http://watson.nci.nih.gov/~zhujack/GEOmetadb.sqlite.gz'

 

I've had the same problem with sradb for a while, until the links has been changed for a aws repository.

 

My session info:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)


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=en_US.UTF-8    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] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] raster_2.5-8        sp_1.2-5            SRAdb_1.37.0
 [4] RCurl_1.95-4.8      bitops_1.0-6        graph_1.56.0
 [7] GEOmetadb_1.38.0    RSQLite_2.0         GEOquery_2.46.0
[10] Biobase_2.38.0      BiocGenerics_0.24.0 logging_0.7-103

 

 

best,

 

Arnaud

ADD COMMENTlink modified 11 days ago by Sean Davis21k • written 11 days ago by arnaud.ceol.pro10
3
gravatar for Sean Davis
11 days ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Sorry for the recent instability. We have switched the GEOmetadb package over to AWS hosting as we did with SRAdb. I just made the change to GEOmetadb in both release and devel, so expect the change to be available from bioconductor in about 36 hours or so. If you need something sooner, installing from github ('seandavi/GEOmetadb') should get you the fix now. 

 

ADD COMMENTlink written 11 days ago by Sean Davis21k
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