Question

Cannot download GEOmetadb sqlite file

1

Entering edit mode

arnaud.ceol.pro ▴ 10

@arnaudceolpro-14348

Last seen 7.1 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

GEOmetadb • 2.4k views

ADD COMMENT • link updated 3 months ago by Pablo • 0 • written 7.1 years ago by arnaud.ceol.pro ▴ 10

score 3 · Accepted Answer · 2017-11-09

3

Entering edit mode

Sean Davis 21k

@sean-davis-490

Last seen 4 months ago

United States

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 COMMENT • link 7.1 years ago Sean Davis 21k

1

Entering edit mode

Sadly it seems like it's not fixed yet in package.version("GEOmetadb") [1] "1.58.0":

if( !file.exists("GEOmetadb.sqlite") ) {
        demo_sqlfile <- getSQLiteFile(destdir = getwd(), destfile = "GEOmetadb.sqlite.gz", type = "demo")
    } else {
        demo_sqlfile <- "GEOmetadb.sqlite"
    }
trying URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb_demo.sqlite.gz'
Error in download.file(url_geo, destfile = localfile, mode = "wb") : 
  cannot open URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb_demo.sqlite.gz'
In addition: Warning message:
In download.file(url_geo, destfile = localfile, mode = "wb") :
  cannot open URL 'http://starbuck1.s3.amazonaws.com/sradb/GEOmetadb_demo.sqlite.gz': HTTP status was '403 Forbidden'

ADD REPLY • link 2.4 years ago António Miguel de Jesus Domingues ▴ 510

0

Entering edit mode

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?

ADD REPLY • link 10 months ago ilayahari • 0

0

Entering edit mode

I checked and the fixed in the developer version from Github. You can install it with remote:

remotes::install_github("https://github.com/zhujack/GEOmetadb.git")

ADD REPLY • link 3 months ago Pablo • 0