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

[Hardcastle, Justin]

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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