[BioC] Cevap: Re: SRAdb error

[Dan Tenenbaum]

Hi Ayten,

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
> below.
> Could you write what was wrong or what I should do?
>
>  Thanks again.
>
> Dr. Ayten Yiğiter
> Hacettepe University
> Faculty of Science
> Department of Statistics
> Ankara/Turkey
> Phone: +90 312 2977900
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
> locale:
> [1] LC_COLLATE=Turkish_Turkey.1254  LC_CTYPE=Turkish_Turkey.1254
> [3] LC_MONETARY=Turkish_Turkey.1254 LC_NUMERIC=C
> [5] LC_TIME=Turkish_Turkey.1254
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] SRAdb_1.8.0    RCurl_1.91-1.1 bitops_1.0-4.1 graph_1.32.0
> RSQLite_0.11.1
> [6] DBI_0.2-5
> loaded via a namespace (and not attached):
> [1] 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()
I get:
trying URL 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz'
Content type 'application/octet-stream' length 187043912 bytes (178.4 Mb)
opened URL
================================================
downloaded 178.4 Mb

Unzipping...

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.

Dan


> 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:
>>
>>
>> library(SRAdb)
>> 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
>> Unzipping...
>> 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
> sessionInfo()
> command?
> That will give us the information we need to help you.
> Thanks,
> Dan
>
>
>>
>> Sincerely yours
>>
>> Dr. Ayten Yiğiter
>> Hacettepe University
>> Faculty of Science
>> Department of Statistics
>> Ankara/Turkey
>> Phone: +90 312 2977900
>>
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>
>