[BioC] Unable to open database file, cummeRbund error.

[Kasper Daniel Hansen]

Loyal,

You might want to start using normalizePath() and expand.path() in your code.

Kasper

On Thu, Jun 28, 2012 at 2:30 PM, Hardcastle, Justin <jhardcas at fhcrc.org> wrote:
> I've managed to make it run using the absolute path. I thought I was using the absolute path, but it turns out I could have been more explicit which made it start at least. I'm getting a new error now though. The error is below.
>
> Reading /Volumes/home/Justin/Projects/Test/output/cuffdiff/cds.diff
> Writing CDSDiffData table
> Indexing Tables...
> Error in sqliteExecStatement(con, statement, bind.data) :
>  RS-DBI driver: (error in statement: database is locked)
>
> cds.diff exists and has data, and the permissions on the DB file look fine for my user.
>
> Thanks for any help.
> -Justin
>
> ----- Original Message -----
> From: "Loyal Goff" <lgoff at csail.mit.edu>
> To: "Justin Hardcastle" <jhardcas at fhcrc.org>
> Cc: bioconductor at r-project.org
> Sent: Wednesday, June 27, 2012 7:57:31 AM
> Subject: Re: [BioC] Unable to open database file, cummeRbund error.
>
> Hi Justin,
> Can you confirm that "~/Test/output/cuffdiff" is a valid path?  I cannot seem to re-create this issue using a similar approach to yours.  Alternatively, can you just provide the directory path directly to readCufflinks instead of going through file.path()?
>
> -Loyal
>
>
> On Jun 26, 2012, at 2:03 PM, Hardcastle, Justin wrote:
>
>> Hi,
>> I'm having an issue running cummeRbund on my cuffdiff output. CummeRbund is giving me a DB error and not creating the DB. The code and error are below.
>>
>> library("cummeRbund")
>>
>> dir = "~/Test"
>> outdir = "output/cuffdiff"
>> cuff <- readCufflinks(dir = file.path(dir, outdir), rebuild = TRUE)
>>
>> The error given is
>>
>>> cuff <- readCufflinks(dir = file.path(dir, outdir), rebuild = TRUE)
>> Creating database ~/Test/output/cuffdiff/cuffData.db
>> Error in sqliteNewConnection(drv, ...) :
>>  RS-DBI driver: (could not connect to dbname:
>> unable to open database file
>> )
>>
>> I am running cummeRbund 1.2.0, and Cufflinks 2.0.1.
>>
>> Thanks for any help.
>>
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