[BioC] Problem with AnnotationDbi::loadAnnDbPkgIndex()

cstrato cstrato at aon.at
Sun Jul 25 19:22:06 CEST 2010


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
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
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