[BioC] Cevap: Re: SRAdb error
dtenenba at fhcrc.org
Mon Mar 26 19:30:31 CEST 2012
Let's keep the bioconductor list in this thread because that way more
people have the opportunity to help you.
2012/3/26 Ayten YIGITER <yigiter at hacettepe.edu.tr>:
> Hi Dan,
> Thank you for your helps.
> When I write "sessionInfo()" on the command window, I see the information
> Could you write what was wrong or what I should do?
> Thanks again.
> Dr. Ayten Yiğiter
> Hacettepe University
> Faculty of Science
> Department of Statistics
> Phone: +90 312 2977900
> R version 2.14.1 (2011-12-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>  LC_COLLATE=Turkish_Turkey.1254 LC_CTYPE=Turkish_Turkey.1254
>  LC_MONETARY=Turkish_Turkey.1254 LC_NUMERIC=C
>  LC_TIME=Turkish_Turkey.1254
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  SRAdb_1.8.0 RCurl_1.91-1.1 bitops_1.0-4.1 graph_1.32.0
>  DBI_0.2-5
> loaded via a namespace (and not attached):
>  Biobase_2.14.0 GEOquery_2.20.8 tools_2.14.1 XML_3.9-4.1
As Sean said in an earlier message, you need to provide all the
commands you are running, specifically the one(s) that produce the
error. When I run
sqlfile <- getSRAdbFile()
trying URL 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz'
Content type 'application/octet-stream' length 187043912 bytes (178.4 Mb)
downloaded 178.4 Mb
Metadata associate with downloaded file:
c("schema version", "creation timestamp")c("1.0", "2012-02-29 02:52:37")
I don't get any errors.
> 03/23/12, Dan Tenenbaum <dtenenba at fhcrc.org> yazmış:
> Hi Ayten,
> 2012/3/22 Ayten YIGITER <yigiter at hacettepe.edu.tr>:
>> Hi, I am trying to get the SRAdb package work. I have successfully
>> installed the SRAdb package and then I have got the following error:
>> sqlfile <- getSRAdbFile()
>> URL 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz' deneniyor
>> Content type 'application/octet-stream' length 187043912 bytes (178.4 Mb)
>> URL açıldı
>> downloaded 178.4 Mb
>> Error: sqliteNewConnection(drv, ...) :
>> RS-DBI driver: (could not connect to dbname:
>> unable to open database file"
>> Could you help me at this point?
> Can you post the output of R's
> That will give us the information we need to help you.
>> Sincerely yours
>> Dr. Ayten Yiğiter
>> Hacettepe University
>> Faculty of Science
>> Department of Statistics
>> Phone: +90 312 2977900
>> Bioconductor mailing list
>> Bioconductor at r-project.org
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