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InParanoidBuilder_DB <- function( organism=c("Arabidopsis thaliana","Apis mellifera"),
prefix, pkgPath, version, author
) {
## Build annotation data packages for InParanoid
##
## organism - a string vector with two elements for the name of two organisms.
##
## pkgPath - a character string for the full path of an existing
## directory where the built backage will be stored.
##
## version - a character string for the version number.
##
## author - a list with named elements "authors" containing a character
## vector of author names and "maintainer" containing the complete
## character string for the maintainer field, for example, "Jane
## Doe <jdoe@doe.com>".
##
## Copyright 2008, Hong Li, all rights reserved.
##
if(any(c(missing(organism), missing(prefix), missing(pkgPath),
missing(version), missing(author),
is.null(organism), is.null(prefix), is.null(pkgPath),
is.null(version), is.null(author)))){
stop(paste("Parameters organism, prefix, pkgPath, ",
"version, or author can not be missing or NULL",
sep = ""))
}
if( length(organism)!=2 ){
stop("Parameter organism is not correct, must have two species")
}
pkgName = paste(prefix,"db",sep=".")
srcUrls <- getSrcUrl("InParanoid", organism)
built <- getSrcBuilt("InParanoid", organism)
# create annotation package, and write data into "*.sqlite" file
createEmptyDPkg(pkgName, pkgPath, force = TRUE,
folders = c("man", "R", paste("inst","extdata",sep=.Platform$file.sep) ))
drv <- dbDriver("SQLite")
outputFile <- file.path(pkgPath, pkgName, paste("inst",
"extdata", sep=.Platform$file.sep), paste(prefix, "sqlite", sep="."))
db <- dbConnect(drv, outputFile)
# write data
writeData_DB("INPARANOID", srcUrls, db)
repList <- getRepList_DB(organism=paste(organism,collapse=" ; "),
"INPARANOID", srcUrls, built, pkgName)
writeMeta_DB(db, repList)
dbDisconnect(db)
writeManAnno_DB(pkgName, pkgPath, version, author, repList)
}
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