The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: Cannot download GEOmetadb sqlite file
1
gravatar for arnaud.ceol.pro
15 months 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

geometadb • 258 views
ADD COMMENTlink modified 15 months ago by Sean Davis21k • written 15 months ago by arnaud.ceol.pro10
Answer: Cannot download GEOmetadb sqlite file
3
gravatar for Sean Davis
15 months 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 15 months ago by Sean Davis21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 168 users visited in the last hour