[BioC] Problem with AnnotationDbi::loadAnnDbPkgIndex()

cstrato cstrato at aon.at
Sun Jul 25 19:33:20 CEST 2010


Dear all,

I just realized the example applies to method:
setMethod("makeAnnDbPkg", "AnnDbPkgSeed",
     function(x, dbfile, dest_dir=".", no.man=FALSE, ...)

Sorry for bothering you.
Christian

On 7/25/10 7:22 PM, cstrato wrote:
> Dear all,
>
> I am trying to understand how AnnotationDbi works and have the following
> problem with function loadAnnDbPkgIndex():
>
> 1, This works ok:
>
>  > tmp <- loadAnnDbPkgIndex()
>  > dim(tmp)
> [1] 123 14
>
>
> 2, However, the following results in an error:
>
>  > tmp <-
> loadAnnDbPkgIndex("/Volumes/CoreData/CRAN/Bioconductor/packages/hu6800.db/inst/extdata/hu6800.sqlite")
>
> Error in read.dcf(tmp_file) :
> Line starting 'SQLite format 3 ...' is malformed!
> In addition: Warning message:
> In readLines(infile, n = 1) :
> incomplete final line found on
> '/Volumes/CoreData/CRAN/Bioconductor/packages/hu6800.db/inst/extdata/hu6800.sqlite'
>
>
>
> Maybe, I misunderstand something but the help file for makeAnnDbPkg()
> has the following example:
>
>  > makeAnnDbPkg(seed, "path/to/hgu133a2.sqlite")
>
> Looking at the source code of makeAnnDbPkg() I get:
>
> setMethod("makeAnnDbPkg", "character",
> function(x, dbfile, dest_dir=".", no.man=FALSE, ...)
> {
> if (missing(dbfile)) {
> dbfile <- system.file("extdata", "GentlemanLab", "ANNDBPKG-INDEX.TXT",
> package="AnnotationDbi")
> }
> index <- loadAnnDbPkgIndex(dbfile)
> etc
> }
>
> As you see 'dbfile="path/to/hgu133a2.sqlite"' is passed directly to
> loadAnnDbPkgIndex(dbfile).
> Do I miss something?
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
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