[BioC] problem with AnnotationDbi

[hpages at fhcrc.org]

Hi Mark,

Quoting Mark Kimpel <mwkimpel at gmail.com>:

[...]
> Error in sqliteExecStatement(con, statement, bind.data) :
>   RS-DBI driver: (error in statement: table metadata already exists)

I guess the code you are running has been designed to generate an .sqlite
file from scratch. So it probably assumes that you don't already have this
file on disk. What happens is that, if this file doesn't exist, then
dbConnect() (which is called internally by makeRATCHIP_DB()) will create
it, otherwise it will open the existing one. If the existing file already
contains the 'metadata' table (or any other table that makeRATCHIP_DB()
needs to create) then you'll get an error like the one you got.

In your case it looks like you already have an old .sqlite file that
probably results from a previous attempt to run makeRATCHIP_DB().
Make sure you remove it (you'll need to figure out where it is) before
you run makeRATCHIP_DB() again.

Cheers,
H.

>
> Enter a frame number, or 0 to exit
>
> 1: makeRATCHIP_DB(affy = FALSE, prefix = "ragene10stv1", fileName =   
> "RaGene-1_
> 2: popRATCHIPDB(affy = affy, prefix = prefix, fileName = fileName, chipMapSrc
> 3: getMapForOtherChipPkg(filePath = fileName, pkgName = prefix,   
> chipMapSrc = c
> 4: probe2gene(baseMap = baseMap, baseMapType = baseMapType, otherSrc  
>  = otherSr
> 5: sqliteQuickSQL(db, "CREATE TABLE metadata (name VARCHAR(80)   
> PRIMARY KEY, va
> 6: sqliteExecStatement(con, statement, bind.data)
>
> Selection: c
> Enter an item from the menu, or 0 to exit
> Selection: 0
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] RSQLite_0.7-0       DBI_0.2-4           AnnotationDbi_1.4.0
> [4] affy_1.20.0         Biobase_2.2.0       graph_1.20.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.10.0        cluster_1.11.11      preprocessCore_1.4.0
>>
> ------------------------------------------------------------
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
>
> 15032 Hunter Court, Westfield, IN  46074
>
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219  Home
> Skype:  mkimpel
>
> "The real problem is not whether machines think but whether men do."
> -- B. F. Skinner
>
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