Entering edit mode
arnaud.ceol.pro
▴
10
@arnaudceolpro-14348
Last seen 6.9 years ago
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
Sadly it seems like it's not fixed yet in
package.version("GEOmetadb") [1] "1.58.0"
:I am facing the same issue, i am unable to download the GEOmetadb.sqlite.gz file from source. Kindly provide suitable solution. Is it available in aws?
I checked and the fixed in the developer version from Github. You can install it with remote: