[Bioc-devel] makeAnnDbPkg (AnnotationDbi)

[James F. Reid]

Dear list,

I am building a custom annotation package using AnnotationDbi and I have 
run into problems using a template package structure that does not 
belong to the the ones supplied under AnnotatioDbi/inst.

For example:

makeAnnDbPkg(myseed, mydbfile, dest_dir = tempdir())
gives
Error in createPackage(x at Package, destinationDir = dest_dir, originDir = 
template_path,  : 'originDir' must be a directory ()

This is because 'myseed' contains a PkgTemplate pointing to my custom 
directory "/myhome/template/mydb".

The devel version of AnnotationDbi (v. 1.9.4) is doing this to assign 
the path to the template directory:
if (!grepl("^/", x at PkgTemplate)[1]) {
     template_path <- system.file("AnnDbPkg-templates",
                                  x at PkgTemplate,
                                  package="AnnotationDbi")
} else {
         template_path <- x at PkgTemplate
}

Another point related to this issue of providing custom pointers for 
annotation packages is the function mydb_dbschema() which only works if 
the schema is present under Annotation/inst/DBSchemas/, I had to 
substitute the code with the following:

@ANNOBJPREFIX at _dbschema <- function() {
     x <- dbconn(datacache)
     schema <- dbmeta(x, "DBSCHEMA")
     version <- dbmeta(x, "DBSCHEMAVERSION")
     cat(readLines(system.file("DBschemas",
                               paste("schemas_", version, sep=""),
                               paste(schema, ".sql", sep=""),
                               package=sprintf("%s.db",
                                               "@ANNOBJPREFIX@"))),
         sep="\n")
}

Best,
James.