Entering edit mode
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/h
u6800.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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