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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor