[BioC] getSRAdbFile cannot open URL

Martin Morgan mtmorgan at fhcrc.org
Wed Sep 12 01:25:32 CEST 2012

On 09/10/2012 01:40 PM, Nicholas Stong wrote:
> Used SRAdb in the past but couldn't load the database today.
>> getSRAdbFile()
> trying URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
> Error in download.file(url_sra, destfile = localfile, mode = "wb", method =
> method) :
>    cannot open URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'

this 'worked for me'; maybe it was transient or you're behind a 
firewall? Can you access the url in a web browser?


 > sessionInfo()
R version 2.15.1 Patched (2012-08-26 r60438)
Platform: x86_64-unknown-linux-gnu (64-bit)

  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [7] LC_PAPER=C                 LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] SRAdb_1.10.0        RCurl_1.91-1        bitops_1.0-4.1
[4] graph_1.34.0        RSQLite_0.11.1      DBI_0.2-5
[7] BiocInstaller_1.4.7

loaded via a namespace (and not attached):
[1] Biobase_2.16.0     BiocGenerics_0.2.0 GEOquery_2.23.5 
[5] XML_3.9-4

> I see that this backup database url is not found, and the primary URL,
> http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz, says forbidden.  Is
> this version and links out of date?  Any help would be appreciated.
> Nick

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